├── docs ├── CNAME ├── images │ ├── Levi.png │ ├── Aedin.jpg │ ├── Laurent.jpg │ ├── SeanDavis.png │ ├── favicon.ico │ ├── PeterHickey.jpg │ ├── KellyRuggles.jpeg │ ├── LorenaPantano.jpeg │ ├── MartinMorgan.jpg │ ├── MatthewMcCall.jpeg │ ├── VincentCarey.jpg │ ├── VincentCarey.png │ ├── WolfgangHuber.jpg │ ├── PariksheetNanda.jpg │ ├── ThomasSCarroll.jpeg │ ├── sponsors │ │ ├── ru-logo.png │ │ ├── genentech.jpg │ │ ├── rpci-logo_1.png │ │ ├── PrimeDiscoveries.png │ │ ├── F1000R_logo_header.png │ │ ├── RU_logo_tagline294.jpg │ │ ├── novartis_logo_pos_rgb.png │ │ ├── NYU-Langone-Health-768x402.jpg │ │ ├── RStudio-Logo-Blue-Gray-250.png │ │ └── RConsortium_Vertical_Pantone.png │ ├── logo_bioconductor.gif │ ├── speakers │ │ ├── RobPatro.jpg │ │ ├── SiminaBoca.jpg │ │ ├── SiminaBoca.png │ │ ├── JeffreyLeek.jpg │ │ ├── AnshulKundaje.jpg │ │ ├── LievenClement.jpg │ │ ├── LievenClement.png │ │ ├── LihuaJulieZhu.jpg │ │ └── ElliPapaemmanuil.jpg │ └── ThomasSCarroll_headshot.png ├── Gemfile ├── assets │ ├── fonts │ │ ├── Noto-Sans-700 │ │ │ ├── Noto-Sans-700.eot │ │ │ ├── Noto-Sans-700.ttf │ │ │ ├── Noto-Sans-700.woff │ │ │ ├── Noto-Sans-700.woff2 │ │ │ └── Noto-Sans-700.svg │ │ ├── Noto-Sans-italic │ │ │ ├── Noto-Sans-italic.eot │ │ │ ├── Noto-Sans-italic.ttf │ │ │ ├── Noto-Sans-italic.woff │ │ │ └── Noto-Sans-italic.woff2 │ │ ├── Noto-Sans-regular │ │ │ ├── Noto-Sans-regular.eot │ │ │ ├── Noto-Sans-regular.ttf │ │ │ ├── Noto-Sans-regular.woff │ │ │ └── Noto-Sans-regular.woff2 │ │ └── Noto-Sans-700italic │ │ │ ├── Noto-Sans-700italic.eot │ │ │ ├── Noto-Sans-700italic.ttf │ │ │ ├── Noto-Sans-700italic.woff │ │ │ └── Noto-Sans-700italic.woff2 │ ├── js │ │ └── scale.fix.js │ └── css │ │ └── style.css ├── _config.yml ├── registration-cancel.md ├── registration-finish.md ├── scholarships.md ├── workshops.md ├── registration.md ├── call-for-abstracts.md ├── sponsor.md ├── schedule-gentleman-day.md ├── organizers.md ├── schedule-developer-day.md ├── workshop-syllabus.md ├── schedule-day-two.md ├── schedule-day-one.md ├── _layouts │ └── default.html ├── index.md ├── Gemfile.lock ├── posters.md ├── code_of_conduct.md ├── travel-accommodations.md └── talks-community.md ├── .gitignore └── README.md /docs/CNAME: -------------------------------------------------------------------------------- 1 | bioc2019.bioconductor.org -------------------------------------------------------------------------------- /docs/images/Levi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/images/Levi.png -------------------------------------------------------------------------------- /docs/images/Aedin.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/images/Aedin.jpg -------------------------------------------------------------------------------- /docs/images/Laurent.jpg: 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4 | June 24 - 27, New York City, USA. 5 | theme: jekyll-theme-minimal -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.woff -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.woff2 -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.eot -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.ttf -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.woff -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.woff2 -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.eot -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.ttf -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.woff -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BioC2019/devel/docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.woff2 -------------------------------------------------------------------------------- /docs/registration-cancel.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | **Registration Cancelled** 17 | 18 | - [Start over][1]. 19 | - View the [schedule][2]. 20 | - Questions? Send [email][3]. 21 | 22 | [1]: ./registration 23 | [2]: ./schedule 24 | [3]: mailto:bioc2019@bioconductor.org?subject=BioC%202018%20registration 25 | -------------------------------------------------------------------------------- /docs/registration-finish.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | **Registration successful** 17 | 18 | - Submit a [talk, poster, workshop, or birds-of-a-feather][2] abstract. 19 | - View the [schedule][1] for updated speakers and workshops. 20 | - Follow [#bioc2019][tweet] for late-breaking announcements. 21 | 22 | Remember to arrange your own lodging. See you in Toronto! 23 | 24 | [1]: ./schedule 25 | [2]: ./call-for-abstracts 26 | -------------------------------------------------------------------------------- /docs/assets/js/scale.fix.js: -------------------------------------------------------------------------------- 1 | (function(document) { 2 | var metas = document.getElementsByTagName('meta'), 3 | changeViewportContent = function(content) { 4 | for (var i = 0; i < metas.length; i++) { 5 | if (metas[i].name == "viewport") { 6 | metas[i].content = content; 7 | } 8 | } 9 | }, 10 | initialize = function() { 11 | changeViewportContent("width=device-width, minimum-scale=1.0, maximum-scale=1.0"); 12 | }, 13 | gestureStart = function() { 14 | changeViewportContent("width=device-width, minimum-scale=0.25, maximum-scale=1.6"); 15 | }, 16 | gestureEnd = function() { 17 | initialize(); 18 | }; 19 | 20 | 21 | if (navigator.userAgent.match(/iPhone/i)) { 22 | initialize(); 23 | 24 | document.addEventListener("touchstart", gestureStart, false); 25 | document.addEventListener("touchend", gestureEnd, false); 26 | } 27 | })(document); 28 | -------------------------------------------------------------------------------- /docs/scholarships.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Scholarships 17 | 18 | Scholarships are available and targeted toward _Bioconductor_ package 19 | developers and contributors. Scholarships cover registration, travel 20 | (up to $500 per person), and accommodation. All scholarship recipients 21 | must present a talk or poster. To apply for a scholarship, complete 22 | the [Poster / Talk Submission Form][]. 23 | 24 | Key dates for scholarships: 25 | 26 | - Thursday March 15, 2019: Abstract Submissions opens. 27 | - Thursday May 17, 2019: Abstract Submission deadline. 28 | - Thursday May 31, 2019: Notification of talk, poster acceptance. 29 | 30 | [Poster / Talk Submission Form]: https://goo.gl/forms/meoGgX7eipL2ZHKD2 31 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | This repository contains material for the _Bioconductor_ annual 2 | conference. [View the conference web site][1]. 3 | 4 | Edit or add material as markdown files in the docs/ directory. Please 5 | wrap lines to 80 character width and aim for simple markdown rather 6 | than elaborate html or other content. 7 | 8 | Please follow best practices by previewing changes locally. 9 | 10 | 1. Make sure that ruby and bundler are installed, following the 11 | 'Requirements' section of [GitHub's documentation][2]. 12 | 13 | 2. Clone the repository and switch to the `docs/` directory 14 | 15 | cd BioC2019/docs 16 | 17 | 3. Install or update bundler to install the ruby pre-requisities. 18 | 19 | gem install --user-install bundler 20 | # If the installer complains, add the suggested $PATH_TO_RUBY/bin 21 | # directory to your ~/.bash_profile or ~/.bashrc or similar. 22 | 23 | 4. Install ruby pre-requisites. 24 | 25 | bundle install --path vendor/bundle # once only; references Gemfile 26 | 27 | 5. Execute the jekyll server 28 | 29 | bundle exec jekyll serve 30 | 31 | and view the results at https://localhost:4000 32 | 33 | [1]: https://bioconductor.github.io/BioC2019 34 | [2]: https://help.github.com/articles/setting-up-your-github-pages-site-locally-with-jekyll/#requirements 35 | -------------------------------------------------------------------------------- /docs/workshops.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Twitter: [#bioc2019][tweet] 10 | 11 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 12 | [venue]: ./travel-accommodations 13 | 14 | ## Workshops 15 | 16 | Join the _[Bioconductor][]_ Community Slack and #bioc2019-workshops 17 | channel for up-to-date information. 18 | 19 | - [Main Conference](#main-conference) 20 | - [Developer Day](#developer-day) 21 | 22 | ### Main Conference 23 | 24 | Workshops will be announced in April based on submissions to the ([call for workshops, talks, posters, and travel awards][call]). See the [BioC2018 workshops][bioc2018workshops] as a guide. Bioconductor will offer the "100-level" courses every year: 25 | 26 | - _100: R and [Bioconductor][] for everyone: an introduction_ 27 | - _101: Introduction to [Bioconductor][] annotation resources_. 28 | - _102: Solving common bioinformatic challenges using [GenomicRanges][]_. 29 | - _103: Public Data Resources and [Bioconductor][]_. 30 | 31 | 32 | [call]: ./travel-accommodations 33 | [bioc2018workshops]: https://bioconductor.github.io/BiocWorkshops/ 34 | [Bioconductor]: https://bioconductor.org/ 35 | [GenomicRanges]: https://bioconductor.org/packages/GenomicRanges 36 | -------------------------------------------------------------------------------- /docs/registration.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Registration 17 | 18 | REGISTRATION FOR THE MAIN CONFERENCE is **full**; a [waitlist][] is 19 | available. 20 | 21 | Space is still available for the Robert Gentleman Symposium. There is 22 | a fee for this symposium. 23 | 24 | Existing main conference registrations include: 25 | 26 | : - Admission to conference facilities for Developer Day and Main 27 | Conference (June 24-26). 28 | - Continental breakfast, lunch, and light hors d'oeuvres, as well as 29 | morning and afternoon coffee breaks. 30 | 31 | [waitlist]: https://forms.gle/y7v53HPbw5cfHt556 32 | 33 | ## Travel and accommodation 34 | 35 | Participants must arrange and pay for their own travel and 36 | accommodation. 37 | 38 | ## Fees 39 | 40 | Robert Gentleman Symposium (June 27) 41 | : - Academic and not-for-profit: $90. Commercial: $120. 42 | 43 | ## Register now! 44 | 45 | Registration is full; see you next year! 46 | -------------------------------------------------------------------------------- /docs/call-for-abstracts.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Call for F1000Research articles 17 | 18 | Following on from previous years, we are inviting conference attendees to 19 | contribute articles on Bioconductor workflows or packages to the [Bioconductor 20 | gateway]. This is a great opportunity to get credit for your work and increase 21 | its visibility and impact. The submission deadline is **5th July 2019**. 22 | 23 | ## Key Dates 24 | 25 | | Date | What | 26 | | -------- | -------------------------------------- | 27 | | ~~March 15~~ | ~~Deadline for proposals for talks, workshops, early posters, and travel scholarships~~ | 28 | | ~~March 30~~ |~~Notification of decision~~ | 29 | | ~~June 10~~ | ~~Deadline for late posters and for Birds of a Feather meetings~~ | 30 | | ~~June 12~~ | ~~Notification of decision for late posters~~ | 31 | 32 | ## Call for late posters -- CLOSED 33 | 34 | ## Call for Birds of a Feather / Special Interest Groups -- CLOSED 35 | 36 | [Bioconductor gateway]: https://f1000research.com/gateways/bioconductor/about-this-gateway 37 | 38 | 39 | -------------------------------------------------------------------------------- /docs/sponsor.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Sponsor Opportunities 17 | 18 | Interested in sponsoring this conference? Please contact 19 | Martin.Morgan@RoswellPark.org. 20 | 21 | Three levels of sponsorship are available. Sponsors of any level will 22 | be entitled to present a scientific poster during poster sessions. 23 | 24 | - Gold: $7,500 USD -- Up to 8 free registrations. Recognition in 25 | promotional and scheduling material. Sponsored session (e.g., 26 | 'Morning talks', 'Afternoon workshops'). 27 | 28 | - Silver: $5,000 USD -- Up to 5 free registrations. Recognition in 29 | promotional and scheduling material. Sponsored food or social event 30 | (e.g., 'breakfast', 'lunch', 'poster session', 'reception'). 31 | 32 | - Bronze: $2,500 USD. Up to 2 free registrations. Recognition in 33 | promotional and scheduling material. 34 | 35 | Approximate conference demographics: 36 | 37 | - 150+ participants from the global bioinformatics community. 38 | 39 | - Academic (50%), corporate (e.g., pharmaceutical; 30%); 40 | not-for-profit (e.g., Cancer Center; 15%), and government (5%) 41 | participants. 42 | 43 | - Lab / group leaders (10%), postdoctoral researchers (40%), 44 | bioinformatics core staff (20%), and graduate students (30%). 45 | 46 | - PhD (60%), MS (20%), and other degrees. 47 | 48 | - Thought leaders contributing to leading-edge methodological 49 | development, hands-on practitioners incorporating _R_ / 50 | _Bioconductor_ into robust work flows, and researchers developing 51 | bespoke solutions. 52 | -------------------------------------------------------------------------------- /docs/schedule-gentleman-day.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Robert Gentleman Symposium (June 27) 17 | 18 | Robert Gentleman is one of the original authors of the R language and 19 | founder of the Bioconductor project. This special symposium day is 20 | being organized for Robert Gentleman's 60th birthday, in honor of his 21 | wide-ranging and influential contributions to statistical computing 22 | and computational biology. 23 | 24 | The symposium and receiption will be held in Weiss East (the lunch 25 | area during the main conference), Rockfeller University. 26 | 27 | 8:30 - 9:00 -- Registration and breakfast 28 | : 29 | 30 | 9:00 - 9:30 -- Welcome / opening remarks 31 | : + Wolfgang Huber and Levi Waldron 32 | 33 | 9:30 - 10:30 -- Short talks 34 | : + Vincent Carey – Harvard 35 | + Denise Scholtens – NorthWestern / Chicago 36 | + Dave Harrington – DFCI / Harvard 37 | + Leonard Goldstein – Genentech / SF 38 | + Martin Morgan - Roswell Park / NY 39 | + Wolfgang Huber - EMBL / Heidelberg 40 | 41 | 10:30 - 11:00 -- Break 42 | : 43 | 44 | 11:00 - 11:20 -- Evolution of the _R_ / _Bioconductor_ communities 45 | : + Wolfgang Huber - EMBL / Heidelberg 46 | + Aedin Culhane - DFCI / Harvard 47 | 48 | 11:20 - 12:00 -- Short talks 49 | : + Rafael Irizarry - Harvard 50 | + Seth Falcon – BlaBlaCar / Paris 51 | + Thomas Wu – Genentech / SF 52 | + Thomas Lumley – University of Auckland 53 | 54 | 12:00 - 1:30 -- Lunch 55 | : 56 | 57 | 1:30 - 2:30 -- Short talks 58 | : + Richard Bourgon – Genentech / SF 59 | + Jeff Gentry – Broad Institute 60 | + Gabe Becker – Genentech / SF 61 | + Patrick Aboyoun – Nanostring / Seattle 62 | + Josh Kaminker – Genentech / SF 63 | + Simon Tavaré - New York Genome Center 64 | 65 | 2:30 - 3:00 -- Break 66 | : 67 | 68 | 3:00 - 3:45 -- Founders of _R_ and _Bioconductor_ panel discussion 69 | : 70 | 71 | 4:00 - 5pm -- Free public keynote talk by Robert Gentleman 72 | : 73 | 74 | 5:00 - 7:00pm -- Reception 75 | : 76 | 77 | -------------------------------------------------------------------------------- /docs/organizers.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Organizing committee 17 | 18 | 19 | | Photo | Name | Affiliation | 20 | |---|---|---| 21 | | | Kelly Ruggles | Director Academic Programs, Sackler Institute of Graduate Biomedical Sciences and Assistant Professor of Medicine, NYU School of Medicine | 22 | | | Thomas S. Carroll | Head of Bioinformatics, The Rockefeller University | 23 | | | Pariksheet Nanda | PhD student, Genetics and Genomics, University of Connecticut | 24 | | | Lorena Pantano | Research Scientist, Biostatistic department at the Harvard TH Chan School of Public Health | 25 | | | Matthew McCall | Assistant Professor of Biostatistics and Biomedical Genetics, University of Rochester Medical Center | 26 | | | Peter Hickey | Senior Research Officer, Walter and Eliza Hall Institute of Medical Research, Australia | 27 | | | Levi Waldron | Associate Professor of Biostatistics, Graduate School of Public Health and Health Policy and Institute for Implementation Science in Public Health, City University of New York| 28 | | | Martin Morgan | Professor, Roswell Park Comprehensive Cancer Center. Project leader, Bioconductor | 29 | | | Aedin Culhane | Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health | 30 | | | Laurent Gatto | Professor of bioinformatics, de Duve Institute, UCLouvain, Belgium | 31 | | | Sean Davis | Senior Associate Scientist, Center for Cancer Research, National Cancer Institute | 32 | | | Vince Carey | Professor of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School | 33 | | | Wolfgang Huber | Group Leader and Senior Scientist, EMBL Heidelberg, Germany | 34 | -------------------------------------------------------------------------------- /docs/schedule-developer-day.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | # Developer Day: Monday June 24 17 | 18 | 19 | 20 | 8:30 - 9:00 -- Registration and breakfast -- Farkas Breezeway 21 | : 22 | 23 | 9:00 - 9:30 -- Welcome -- Farkas Auditorium 24 | : [Orientation & project updates][1] 25 | 26 | 9:30 - 10:00 -- Rob Patro -- Farkas Auditorium 27 | : 28 | 29 | 10:00 - 10:30 -- Lightning talks I -- Farkas Auditorium 30 | : Any Developer Day attendee can present a lightning talk (short 5 31 | minute presentations); be prepared to volunteer on the day of the 32 | conference. [Sign up now][]! 33 | 34 | 10:30 - 11:00 -- Break, newcomers / old-timers meet-up -- Farkas Breezeway 35 | : 36 | 37 | 11:00 - 12:00 -- Birds-of-a-feather I / Workshops I 38 | : + Track 1: [Bioconductor on Containers](http://biocworkshops2019.bioconductor.org.s3-website-us-east-1.amazonaws.com/page/BioconductorOnContainers__Bioconductor_Containers_Workshop/) -- Nitesh Turaga -- Smilow Seminar Room 39 | + Track 2: Common Workflow Language (CWL) workshop[^port8080] -- Daniela 40 | Cassol, Thomas Girke, Marko Zecevic, and Qiang Hu -- SB G19 41 | + Track 3: Lazy representation of very large genomic data resources 42 | in R/Bioconductor -- Qian Liu, Hervé Pagès, and 43 | Martin Morgan -- Farkas Auditorium 44 | + Track 4: [Cloud-scale genomic data science with Bioconductor](http://biocworkshops2019.bioconductor.org.s3-website-us-east-1.amazonaws.com/page/BiocCloudws__cloudScale2019/) -- 45 | Vincent Carey -- MSB Large 46 | 47 | 12:00 - 1:00 -- Lunch -- Farkas Breezeway and outside 48 | : 49 | 50 | 1:00 - 2:00 -- Birds-of-a-feather II / Workshops II 51 | : + Track 1: [Bioconductor on Containers](http://biocworkshops2019.bioconductor.org.s3-website-us-east-1.amazonaws.com/page/BioconductorOnContainers__Bioconductor_Containers_Workshop/) -- Nitesh Turaga -- Smilow Seminar Room 52 | + Track 2: Common Workflow Language (CWL) workshop[^port8080] -- Daniela 53 | Cassol, Thomas Girke, Marko Zecevic, and Qiang Hu -- SB G19 54 | + Track 3: Lazy representation of very large genomic data resources 55 | in R/Bioconductor -- Qian Liu, Hervé Pagès, and 56 | Martin Morgan -- Farkas Auditoriume 57 | + Track 4: [motifStack: plot multiple motifs in one figure](http://biocworkshops2019.bioconductor.org.s3-website-us-east-1.amazonaws.com/page/motifStackWorkshop__motifStackWorkshop/) -- 58 | Jianhong Ou and Lihua Julie Zhu -- MSB Large 59 | 60 | [^port8080]: This workshop is available on your AMI by using port 8080 and logging in as `ubuntu`:`bioc`. 61 | 62 | 2:00 - 2:30 -- Lightning talks II -- [Sign up now][]! -- Farkas Auditorium 63 | : 64 | 65 | 2:30 - 3:00 -- Break -- Farkas Breezeway 66 | : 67 | 68 | 3:00 - 3:30 -- Lightning talks III -- [Sign up now][]! -- Farkas Auditorium 69 | : 70 | 71 | 3:30 - 4:30 -- Birds-of-a-feather / Breakout sessions 72 | : + [Extending gene set and signature representations][2] -- Farkas 73 | + [Bioconductor Infrastructure for Base Modifications][3] -- Smillow Seminar Room 74 | + [Annotation Harmonization][4] -- Farkas Patio 75 | 76 | 4:30 - 5:00 -- Panel discussion -- Farkas Auditorium 77 | : + Project directions and opportunities 78 | 79 | 5:30 -- Outing -- stroll and foraged food in Central Park. 80 | : + Meet in *Grand Army Plaza* at the large golden statue of General 81 | Sherman on a horse behind a lady holding a branch. It's the very 82 | southeast corner of the park at 59th St and 5th Ave. 83 | 84 | [DEVELOPER DAY NOTES]: https://docs.google.com/document/d/1GQFxNRLsO6_2LQjeyXAkWZpkKlFL2_xfo1LbKoBOwzk/edit?usp=sharing 85 | [Sign up now]: https://forms.gle/1k9eD1ahQnjvew8B7 86 | [1]: https://docs.google.com/presentation/d/1S_e9g5OfpJK51TxiUWTKbqomutCsUJ2qgmio_g_qN-E/edit?usp=sharing 87 | [2]: https://github.com/Bioconductor/BioC2019/issues/25 88 | [3]: https://github.com/Bioconductor/BioC2019/issues/35 89 | [4]: https://github.com/Bioconductor/BioC2019/issues/22 90 | -------------------------------------------------------------------------------- /docs/workshop-syllabus.md: -------------------------------------------------------------------------------- 1 | # Insert Workshop Title 2 | 3 | # Instructor(s) name(s) and contact information 4 | 5 | Provide names and contact information for all instructors. 6 | 7 | # Workshop Description 8 | 9 | Along with the topic of your workshop, include how students can expect 10 | to spend their time. For the description may also include information 11 | about what type of workshop it is (e.g. instructor-led live demo, lab, 12 | lecture + lab, etc.). Instructors are strongly recommended to provide 13 | completely worked examples for lab sessions, and a set of stand-alone 14 | notes that can be read and understood outside of the workshop. 15 | 16 | ## Pre-requisites 17 | 18 | List any workshop prerequisites, for example: 19 | 20 | * Basic knowledge of R syntax 21 | * Familiarity with the GenomicRanges class 22 | * Familiarity with xyz vignette (provide link) 23 | 24 | List relevant background reading for the workshop, including any 25 | theoretical background you expect students to have. 26 | 27 | * List any textbooks, papers, or other reading that students should be 28 | familiar with. Include direct links where possible. 29 | 30 | ## Workshop Participation 31 | 32 | Describe how students will be expected to participate in the workshop. 33 | 34 | ## _R_ / _Bioconductor_ packages used 35 | 36 | List any _R_ / _Bioconductor_ packages that will be explicitly covered. 37 | 38 | ## Time outline 39 | 40 | An example for a 45-minute workshop: 41 | 42 | | Activity | Time | 43 | |------------------------------|------| 44 | | Packages | 15m | 45 | | Package Development | 15m | 46 | | Contributing to Bioconductor | 5m | 47 | | Best Practices | 10m | 48 | 49 | # Workshop goals and objectives 50 | 51 | List "big picture" student-centered workshop goals and learning 52 | objectives. Learning goals and objectives are related, but not the 53 | same thing. These goals and objectives will help some people to decide 54 | whether to attend the conference for training purposes, so please make 55 | these as precise and accurate as possible. 56 | 57 | *Learning goals* are high-level descriptions of what 58 | participants will learn and be able to do after the workshop is 59 | over. *Learning objectives*, on the other hand, describe in very 60 | specific and measurable terms specific skills or knowledge 61 | attained. The [Bloom's Taxonomy](#bloom) may be a useful framework 62 | for defining and describing your goals and objectives, although there 63 | are others. 64 | 65 | ## Learning goals 66 | 67 | Some examples: 68 | 69 | * describe how to... 70 | * identify methods for... 71 | * understand the difference between... 72 | 73 | ## Learning objectives 74 | 75 | * analyze xyz data to produce... 76 | * create xyz plots 77 | * evaluate xyz data for artifacts 78 | 79 | ### A note about learning goals and objectives (#bloom) 80 | 81 | While not a new or modern system for thinking about learning, 82 | [Bloom's taxonomy][1] is one useful framework for understanding the 83 | cognitive processes involved in learning. From lowest to highest 84 | cognitive requirements: 85 | 86 | 1. Knowledge: Learners must be able to recall or remember the 87 | information. 88 | 2. Comprehension: Learners must be able to understand the information. 89 | 3. Application: Learners must be able to use the information they have 90 | learned at the same or different contexts. 91 | 4. Analysis: Learners must be able to analyze the information, by 92 | identifying its different components. 93 | 5. Synthesis: Learners must be able to create something new using 94 | different chunks of the information they have already mastered. 95 | 6. Evaluation: Learners must be able to present opinions, justify 96 | decisions, and make judgments about the information presented, 97 | based on previously acquired knowledge. 98 | 99 | To use Bloom's taxonomy, consider the following sets of verbs and 100 | descriptions for learning objectives: 101 | 102 | 1. Remember: Memorize, show, pick, spell, list, quote, recall, repeat, 103 | catalogue, cite, state, relate, record, name. 104 | 2. Understand: Explain, restate, alter, outline, discuss, expand, 105 | identify, locate, report, express, recognize, discuss, qualify, 106 | covert, review, infer. 107 | 3. Apply: Translate, interpret, explain, practice, illustrate, 108 | operate, demonstrate, dramatize, sketch, put into action, complete, 109 | model, utilize, experiment, schedule, use. 110 | 4. Analyze: Distinguish, differentiate, separate, take apart, 111 | appraise, calculate, criticize, compare, contrast, examine, test, 112 | relate, search, classify, experiment. 113 | 5. Evaluate: Decide, appraise, revise, score, recommend, select, 114 | measure, argue, value, estimate, choose, discuss, rate, assess, 115 | think. 116 | 6. Create: Compose, plan, propose, produce, predict, design, assemble, 117 | prepare, formulate, organize, manage, construct, generate, imagine, 118 | set-up. 119 | 120 | [1]: https://cft.vanderbilt.edu/guides-sub-pages/blooms-taxonomy/ "Bloom's Taxonomy" 121 | -------------------------------------------------------------------------------- /docs/schedule-day-two.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | 5 | # BioC 2019: Where Software and Biology Connect 6 | 7 | When: June 24 - 27, 2019
8 | What: Developer Day, Main Conference, Symposium
9 | Where: [NYU and Rockefeller University][venue], New York City, USA
10 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
11 | Twitter: [#bioc2019][tweet]
12 | 13 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 14 | [venue]: ./travel-accommodations 15 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 16 | 17 | 18 | 24 | 25 | [course AMI]: https://courses.bioconductor.org 26 | [bioc-community slack]: https://bioc-community.herokuapp.com/ 27 | 28 | # Day 2: Wednesday June 26 29 | 30 | 8:00 - 8:30 -- Breakfast -- Abby Lounge 31 | : 32 | 33 | 8:30 - 9:00 -- Lieven Clement -- Caspary Auditorium 34 | : 35 | 36 | 9:00 - 9:30 -- Lihua Julie Zhu -- Caspary Auditorium 37 | : 38 | 39 | 9:30 - 10:00 -- Anshul Kundaje -- Caspary Auditorium 40 | : 41 | 42 | 10:00 - 10:30 -- Break -- CRC Lower Level 43 | : 44 | 45 | 10:30 - 12:00 -- Contributed talks Session 4a -- Software focus -- Caspary Auditorium 46 | : + Nitesh Turaga -- 3 reasons to "Bioconductor" on containers 47 | + Vincent Carey -- Bioconductor at "cloud scale" 48 | + Stuart Lee -- Tidy coverage analysis with superintronic and 49 | plyranges 50 | + Nathan Sheffield -- BiocProject, a new Bioconductor-oriented 51 | project management class 52 | + Karun Rajesh -- Storage and Analysis of Microbiome Quality Control 53 | Project Data through phyloseq Package 54 | + Ana Beatriz Villaseñor-Altamirano -- PulmonDB with an accessible 55 | web interface of integrated and curated public transcriptomic data 56 | for the understanding of lung diseases 57 | + Christopher Wilks -- Snapcount: rapid and flexible querying of 58 | over 70,000 gene, exon, and splice junction expression summaries 59 | 60 | 10:30 - 12:00 -- Contributed talks Session 4b -- Biological focus -- Carson Auditorium 61 | : + Benjamin Haibe-Kains -- mCI: Robust biomarker discovery from 62 | cancer pharmacogenomic data 63 | + Aedin Culhane -- Discovery of cancer immune molecular subtypes 64 | + Joselyn Cristina Chavez Fuentes -- A collaborative approach to 65 | improve access to bacterial regulatory networks using 66 | R/Bioconductor. 67 | + Robert Castelo -- RNA sequencing and mass spectometry proteomics 68 | of neonatal dried blood spots 69 | + Cesar Miguel Valdez Cordova -- histoneSig: working with continuous 70 | signal representations from the genome 71 | + Antonio Colaprico -- DeepBlueR and MoonlightR 72 | + Charlotte Soneson -- On the characterisation of complex 73 | transcriptomes with Nanopore native RNA sequencing 74 | 75 | 12:00 - 1:00 -- Lunch / Birds-of-a-feather -- Weiss South Room 76 | : 77 | 78 | 1:00 - 1:50 -- [Workshop Session] 5a 79 | : + The Basics: Introduction to Bioconductor Annotation Resources -- 80 | Lori Shepherd and Jim MacDonald -- RRB 110 81 | + SingleCell: Analysis of multi-sample multi-group scRNA-seq data -- 82 | Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, and Mark 83 | Robinson -- Carson Auditorium 84 | + RNAseq & Omics: Using the recount2 resource and related tools -- 85 | Collado-Torres L, Nellore A, Jaffe AE -- Weiss 305 86 | + Genomics & Enrichment Analysis: Easy and efficient ensemble gene 87 | set testing with EGSEA -- Alhamdoosh M, Law CW, Tian L, Sheridan 88 | JM, Ng M, Ritchie ME -- Weiss 301 89 | 90 | 2:00 - 2:50 -- [Workshop Session] 5b 91 | : + The Basics: Introduction to Bioconductor Annotation Resources -- 92 | Lori Shepherd and Jim MacDonald -- RRB 110 93 | + SingleCell: Analysis of multi-sample multi-group scRNA-seq data -- 94 | Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, and Mark 95 | D. Robinson -- Carson Auditorium 96 | + RNAseq & Omics: Using the recount2 resource and related tools -- 97 | Collado-Torres L, Nellore A, Jaffe AE -- Weiss 305 98 | + Genomics & Enrichment Analysis: Functional enrichment analysis of 99 | high-throughput omics data -- Ludwig Geistlinger and Levi Waldron -- Weiss 301 100 | 101 | 2:50 - 3:10 -- Break -- Weiss South Room 102 | : 103 | 104 | 3:10 - 4:00 -- [Workshop Session] 6a 105 | : + The Basics: Public data resources and Bioconductor -- Levi 106 | Waldron, Benjamin Haibe-Kains, and Sean Davis -- RBB 110 107 | + SingleCell: iSEE: Interactive visualization of 108 | `SummarizedExperiment` objects -- Kevin Rue-Albrecht and Charlotte 109 | Soneson -- Carson Auditorium 110 | + RNAseq & Omics: RNA-seq analysis is easy as 1-2-3 with limma, 111 | Glimma and edgeR -- Law CW, Alhamdoosh M, Su S, Dong X, Tian L et 112 | al -- Weiss 305 113 | + Genomics & Enrichment Analysis: Integrative pathway analysis with 114 | pathwayPCA -- Odom G, Ban Y, Liu L, Wang L, Chen X -- Weiss 301 115 | 116 | 4:10 - 5:00 -- [Workshop Session] 6b 117 | : + The Basics: Public data resources and Bioconductor -- Levi 118 | Waldron, Benjamin Haibe-Kains, and Sean Davis -- RRB 110 119 | + SingleCell: iSEE: Interactive visualization of 120 | `SummarizedExperiment` objects -- Kevin Rue-Albrecht and Charlotte 121 | Soneson -- Carson Auditorium 122 | + RNAseq & Omics: Epidemiology for Bioinformaticians -- Mirzayi C 123 | and Levi Waldron -- Weiss 305 124 | 125 | 5:30 - 7:30 -- Contributed posters 126 | : + __Group-B posters__ -- Weiss Lobby 127 | + Poster dimensions up to 58 inches wide x 40 inches tall. Individual 128 | poster allocations will be affixed to poster boards. 129 | 130 | [Workshop Session]: https://rebrand.ly/biocworkshops2019 131 | -------------------------------------------------------------------------------- /docs/schedule-day-one.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | 5 | # BioC 2019: Where Software and Biology Connect 6 | 7 | When: June 24 - 27, 2019
8 | What: Developer Day, Main Conference, Symposium
9 | Where: [NYU and Rockefeller University][venue], New York City, USA
10 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
11 | Twitter: [#bioc2019][tweet]
12 | 13 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 14 | [venue]: ./travel-accommodations 15 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 16 | 17 | # Day 1: Tuesday June 25 18 | 19 | 25 | 26 | [course AMI]: https://courses.bioconductor.org 27 | [bioc-community slack]: https://bioc-community.herokuapp.com/ 28 | 29 | 8:00 - 8:45 -- Registration and breakfast -- Abby Lounge 30 | : 31 | 32 | 8:45 - 9:00 -- [Welcoming remarks][welcome] -- Martin Morgan -- Caspary Auditorium 33 | : 34 | 35 | 9:00 - 9:30 -- Jeffrey Leek -- Caspary Auditorium 36 | : 37 | 38 | 9:30 - 10:00 -- Elli Papaemmanuil -- Caspary Auditorium 39 | : 40 | 41 | 10:00 - 10:30 -- Simina Boca -- Caspary Auditorium 42 | : 43 | 44 | 10:30 - 11:00 -- Break -- CRC Lower Level 45 | : 46 | 47 | 11:00 - 12:00 -- Contributed talks Session 1a - Single-cell theme -- Caspary Auditorium 48 | : + Robert A. Amezquita -- Orchestrating Single-Cell Analysis with Bioconductor 49 | + Helena L. Crowell -- Analysis of multi-sample multi-group scRNA-seq data 50 | + Shian Su -- CellBench: A Framework for Evaluating Single Cell Analysis Pipelines 51 | + Stephanie Hicks -- mbkmeans: fast clustering for single cell data using mini-batch k-means 52 | + Deepayan Sarkar -- Gene Set Enrichment Analysis with Multi-omics Data 53 | 54 | 11:00 - 12:00 -- Contributed talks Session 1b - Statistical methods -- Carson Auditorium 55 | : + Nima Hejazi -- Generalized Variance Moderation for Locally 56 | Efficient Estimation in High-Dimensional Biology 57 | + John Lawson -- Coordinate Covariation Analysis (COCOA): 58 | Understanding Interindividual Variation in Data with Genomic 59 | Coordinates 60 | + Ingo Ruczinski -- Detection of rare disease variants in extended pedigrees using RVS 61 | + Svetlana Vinogradova -- ASER: eliminating transcriptome-wide batch 62 | effects results in higher precision in allele-specific expression 63 | measurements 64 | + Katharina Imkeller -- Improving accuracy of phenotype detection in 65 | whole-genome CRISPR screens 66 | 67 | 12:00 - 1:00 -- Lunch / Birds-of-a-feather, sponsored by [F1000 Research][] -- Weiss South Room 68 | : 69 | 70 | 1:00 - 1:50 -- [Workshop Session] 2a 71 | : + The Basics: Bioconductor for Everyone -- Martin Morgan and Lori Shepherd -- RRB 110 72 | + SingleCell: Effectively using the DelayedArray framework to 73 | support the analysis of large data sets -- Pete Hickey -- Carson Auditorium 74 | + RNAseq & Omics: Workflow for Multi-omics Analysis with 75 | MultiAssayExperiment and curatedTCGAData -- Marcel Ramos, Ludwig 76 | Geistlinger, and Levi Waldron -- Weiss 301 77 | + Genomics & Enrichment Analysis: Tools for region-based genomic 78 | analysis -- Nathan Sheffield -- Weiss 305 79 | 80 | 2:00 - 2:50 -- [Workshop Session] 2b 81 | 82 | : + The Basics: Bioconductor for Everyone -- Martin Morgan and Lori 83 | Shepherd -- RRB 110 84 | + SingleCell: Effectively using the DelayedArray framework to 85 | support the analysis of large data sets -- Pete Hickey -- Carson Auditorium 86 | + RNAseq & Omics: Workflow for Multi-omics Analysis with 87 | MultiAssayExperiment and curatedTCGAData -- Marcel Ramos, Ludwig 88 | Geistlinger, and Levi Waldron -- Weiss 301 89 | + Genomics & Enrichment Analysis: Tools for region-based genomic 90 | analysis -- Nathan Sheffield -- Weiss 305 91 | 92 | 2:50 - 3:10 -- Break -- Weiss South Room 93 | : 94 | 95 | 3:10 - 4:00 -- [Workshop Session] 3a 96 | : + The Basics: Fluent genomic workflows with plyranges -- Stuart Lee 97 | -- Weiss 305 98 | + SingleCell: Orchestrating Single-Cell Analysis with Bioconductor: 99 | Overview and Workflows -- Robert A. Amezquita, Vince J. Carey, 100 | Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L.Lun, et al. -- Carson Auditorium 101 | + RNAseq & Omics: Bioinformatics tools for integrating and 102 | understanding molecular changes associated with with Immune 103 | Response, Stemness and Oncogenic processes -- Antonio Colaprico, 104 | Gabriel Odom, Lily Wang, & Xi Chen -- Weiss 301 105 | + Genomics & Enrichment Analysis: Copy number variation analysis 106 | with Bioconductor -- Ludwig Geistlinger, Marcel Ramos, Seyhun Oh, 107 | and Levi Waldron -- RRB 110 108 | 109 | 4:10 - 5:00 -- [Workshop Session] 3b 110 | : + The Basics: A plyranges and tximeta case study: differential 111 | expression and accessibility -- Michael Love -- Weiss 305 112 | + SingleCell: Analysis of large single-cell RNA-seq datasets in 113 | R/Bioconductor -- Davide Risso and Stephanie Hicks -- Carson Auditorium 114 | + RNAseq & Omics: Working with open-source Human Microbiome Project 115 | Data: Efficient Data Access and Analysis Workflow -- Levi Walrdon, 116 | Ni Zhao, Mikhail Dozmorov, Ekaterina Smirnova -- Weiss 301 117 | + Genomics & Enrichment Analysis: ATAC-seq data quality control 118 | using the ATACseqQC package -- Haibo Liu, Jianghong Ou, and Julie 119 | Lihua Zhu -- RRB 110 120 | 121 | 5:30 - 7:30 -- Contributed posters 122 | : + __Group-A posters__ -- Weiss Lobby 123 | + Lightning talks (concurrent with posters) -- Weiss 301 124 | + Poster dimensions up to 58 inches wide x 40 inches tall. Individual 125 | poster allocations will be affixed to poster boards. 126 | 127 | [welcome]: https://docs.google.com/presentation/d/1U76nYf-RMHEJ0Zh9IT39ZqxjuIaeMuxuhd1HmFqLWrQ/edit?usp=sharing 128 | [F1000 Research]: https://f1000research.com/gateways/bioconductor/ 129 | [Workshop Session]: https://rebrand.ly/biocworkshops2019 130 | -------------------------------------------------------------------------------- /docs/_layouts/default.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | {% seo %} 8 | 9 | 10 | 11 | 12 | 13 | 16 | 17 | 18 |
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31 | Conference Home
32 | Registration
33 | Call for submissions
34 | Travel & Accommodation
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36 | Schedule
37 | - Developer Day
38 | - Main Conference -- Day 1
39 | - Main Conference -- Day 2
40 | - Robert Gentleman Symposium
41 | - Poster Titles
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43 | Resources
44 | - Organizing committee
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48 | Sponsor Opportunities
49 | 50 | Code of Conduct
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54 | 55 | Genentech 60 | 61 | Novartis 66 | 67 |
68 | 69 | Prime Discoveries 74 | 75 |
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84 | 85 | RStudio 90 | 91 |
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100 | 101 | Roswell Park Cancer Institute 106 | 107 |
108 | 109 | NYU 114 | 115 |
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125 | Bioconductor: https://bioconductor.org
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138 | 139 | 140 | {% if site.google_analytics %} 141 | 150 | {% endif %} 151 | 152 | 153 | -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | speakers: 4 | - name: Rob Patro 5 | inst: Stony Brook University 6 | url: http://www.robpatro.com/redesign 7 | blurb: "I am an assistant professor in the Computer Science 8 | department at Stony Brook University. My main academic interests 9 | include computational biology and bioinformatics, machine 10 | learning, programming languages, computer graphics, scientific 11 | visualization and parallel computation. I also have recreational 12 | interests in math, physics, music, politics and video games." 13 | - name: Jeffrey Leek 14 | inst: Johns Hopkins University 15 | url: http://jtleek.com/ 16 | blurb: "Dr. Leek leads a group of researchers, educators, and data 17 | scientists using data to solve problems in molecular biology, 18 | human health, meta-research, education, and anything else they 19 | think could be useful for the world. They produce data tools and 20 | code that you can use for your projects as well." 21 | - name: Elli Papaemmanuil 22 | inst: Memorial Sloan Kettering Cancer Center 23 | url: https://www.mskcc.org/research-areas/labs/elli-papaemmanuil 24 | blurb: "The Papaemmanuil lab is a collective of clinical, 25 | computational, molecular and mathematic research investigators 26 | with an interest to study the role of acquired mutations in 27 | cancer development and how these determine clinical phenotype 28 | and response to therapy. Her mission is to execute research that 29 | informs and moves clinical practices in oncology forward." 30 | - name: Simina Boca 31 | inst: Georgetown University 32 | url: https://icbi.georgetown.edu/Boca 33 | blurb: "Dr. Boca analyzes omics data, including metabolomics and 34 | genomics, and considers their downstream application in 35 | precision medicine. In particular, she developed novel 36 | computational and statistical methods for high-dimensional data 37 | analysis, led the first comprehensive metabolomic study for 38 | Duchenne muscular dystrophy, and contributed to several of the 39 | early exome sequencing projects of human tumors. Additional 40 | areas of interest include cancer epidemiology and population 41 | genetics." 42 | - name: Lieven Clement 43 | inst: Ghent University, Belgium. 44 | url: https://statomics.github.io/ 45 | blurb: "The Clement group develops novel statistical methods and 46 | tools for the interpretation of omics data. Their research is 47 | structured according to three ‘omics domain: Meta-genomics, 48 | Transcriptomics (RNA-seq and single cell RNA-seq) and Proteomics 49 | (Identification and Differential Analysis in Mass Spectrometry 50 | based Quantitative Proteomics). They also leverage expertise in 51 | experimental design and data analysis for omics to researchers 52 | in the life sciences and have a keen interest in ‘omics data 53 | integration." 54 | - name: Lihua Julie Zhu 55 | inst: University of Massachusetts 56 | url: https://profiles.umassmed.edu/display/129880 57 | blurb: "Dr. Zhu is interested in the understanding of gene 58 | regulation and cancer etiology, biomarker discovery, and 59 | development and application of genome editing technology by 60 | mining and integrating various high-throughput datasets such as 61 | ChIP-seq, RNA-seq, ATAC-seq, miRNA-seq, Hi-C, shRNA-seq, 62 | PAS-seq, NAD-seq and GUIDE-seq. Her expertise is algorithm and 63 | computational tool development, and her group is an active 64 | contributor to the Bioconductor project. She has developed a 65 | dozen packages with various utilities, ranging from machine 66 | learning, peak calling, motif identification and alignment, 67 | quality assessment of ATACseq data, annotation, data 68 | integration, visualization, gRNA design and genome-wide 69 | offtargets identification in CRISPR genome editing studies." 70 | - name: Anshul Kundaje 71 | inst: Stanford University 72 | url: https://profiles.stanford.edu/anshul-kundaje 73 | blurb: "Anshul Kundaje is an Assistant Professor of Genetics and 74 | Computer Science at Stanford University. His primary research 75 | area is large-scale computational regulatory genomics. The 76 | Kundaje lab specializes in developing statistical and machine 77 | learning methods for large-scale integrative analysis of 78 | heterogeneous, high-throughput functional genomic and genetic 79 | data to decipher regulatory elements and long-range regulatory 80 | interactions, learn predictive regulatory network models across 81 | individuals, cell-types and species and improve detection and 82 | interpretation of natural and disease-associated genetic 83 | variation." 84 | --- 85 | # BioC 2019: Where Software and Biology Connect 86 | 87 | When: June 24 - 27, 2019
88 | What: Developer Day, Main Conference, Symposium
89 | Where: [NYU and Rockefeller University][venue], New York City, USA
90 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
91 | Twitter: [#bioc2019][tweet]
92 | 93 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 94 | [venue]: ./travel-accommodations 95 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 96 | 97 | BioC2019 highlights current developments within and beyond 98 | the [Bioconductor](https://www.bioconductor.org) project. It consists of: 99 | * [Developer Day](./schedule-developer-day) June 24 at NYU Langone: 100 | provides developers and would-be developers with insights into 101 | Bioconductor project direction and software development best 102 | practices. 103 | * [Main Conference](./schedule-day-two) June 25-26 at Rockefeller University: 104 | morning scientific talks and afternoon workshops provide insights 105 | and tools required for the analysis and comprehension of 106 | high-throughput genomic data. 107 | * [Robert Gentleman Symposium](./schedule-gentleman-day) June 27 at 108 | Rockefeller University: A one-time symposium in honor of the 60th 109 | birthday of [Robert 110 | Gentleman](https://en.wikipedia.org/wiki/Robert_Gentleman_(statistician)), 111 | one of the originators of R and Bioconductor. This day will feature 112 | talks and panel discussion by Robert Gentleman and associates. 113 | 114 | 115 | ## Confirmed Speakers 116 | 117 | {% for s in page.speakers %} 118 | {% assign imgpath = "images/speakers/" | append: s.name | remove: ' ' | append: '.jpg' %} 119 | 120 | ### [{{ s.name }}]({{ s.url }}), {{ s.inst }} 121 | 122 | > {{ s.blurb }} 123 | 124 | {% endfor %} 125 | 126 | More information: [workshop@bioconductor.org][contact] 127 | 128 | Tweet #bioc2019 131 | 132 | 133 | 134 | [contact]: mailto:workshop@bioconductor.org?subject=BioC2019%20question 135 | [survey]: https://forms.gle/eRWv3tdXLvxYT2CYA 136 | -------------------------------------------------------------------------------- /docs/Gemfile.lock: -------------------------------------------------------------------------------- 1 | GEM 2 | remote: https://rubygems.org/ 3 | specs: 4 | actionpack (4.2.11.1) 5 | actionview (= 4.2.11.1) 6 | activesupport (= 4.2.11.1) 7 | rack (~> 1.6) 8 | rack-test (~> 0.6.2) 9 | 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(0.7.2) 253 | i18n 254 | ruby_dep (1.5.0) 255 | rubyzip (2.2.0) 256 | safe_yaml (1.0.5) 257 | sass (3.7.4) 258 | sass-listen (~> 4.0.0) 259 | sass-listen (4.0.0) 260 | rb-fsevent (~> 0.9, >= 0.9.4) 261 | rb-inotify (~> 0.9, >= 0.9.7) 262 | sawyer (0.8.1) 263 | addressable (>= 2.3.5, < 2.6) 264 | faraday (~> 0.8, < 1.0) 265 | terminal-table (1.8.0) 266 | unicode-display_width (~> 1.1, >= 1.1.1) 267 | thread_safe (0.3.6) 268 | typhoeus (1.3.1) 269 | ethon (>= 0.9.0) 270 | tzinfo (1.2.5) 271 | thread_safe (~> 0.1) 272 | unicode-display_width (1.5.0) 273 | 274 | PLATFORMS 275 | ruby 276 | 277 | DEPENDENCIES 278 | github-pages 279 | minimal 280 | 281 | BUNDLED WITH 282 | 2.0.1 283 | -------------------------------------------------------------------------------- /docs/posters.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Twitter: [#bioc2019][tweet] 10 | 11 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 12 | [venue]: ./travel-accommodations 13 | 14 | ## Posters 15 | 16 | Poster sessions will be held in __Weiss lobby__ in the 5:30 to 7:30pm sessions in two groups on the __25th (Group A)__ and the __26th (Group B)__ of June. 17 | 18 | Please affix your poster to your allocated poster board during the lunch break session (12-1pm) on the day of presentation and remove posters by 12pm the following day. Poster boards will be allocated with presenters names affixed to the board. 19 | 20 | ### Session 1 - __Group A - 5:30 to 7:30 (25th June) in Weiss lobby__ 21 | 22 | Jianhong Ou\*, Julie Zhu. TrackViewer: Lollipop/dandelion plots for methylation status and mutation data. Keywords: Software, Visualization, VariantAnnotation. 23 | 24 | Lluís Revilla Sancho\*, Pau Sancho-Bru, Juan José Salvatella Lozano. BioCor: a package to measure functional similarities. Keywords: Pathways, StatisticalMethod, SystemsBiology, Similarity, Clustering. 25 | 26 | Carey VJ\*, Stubbs BJ, Gopaulakrishnan S, Pollack S, Davis S. Bioconductor at cloud scale. Keywords: Software, GenomicVariation, CloudComputing, ImmunoOncology. 27 | 28 | Tang M\*, Kaymaz Y, Eichhorn S, Liang Z, Dulac C, Sackton T. Scclusteval: An R package for evaluating single cell RNAseq clustering. Keywords: GeneExpression Transcriptomics Clustering SingleCell. 29 | 30 | Vaestermark AJ, Walters JR\*. Title TBD. Keywords: DataRepresentation, Sequencing, GeneExpression, SystemsBiology, DifferentialExpression. 31 | 32 | Hejazi, NS\*, van der Laan MJ, Hubbard AE. Generalized Variance Moderation for Locally Efficient Estimation in High-Dimensional Biology. Keywords: GeneExpression, DifferentialExpression, Microarray, RNASeq, MultipleComparison. 33 | 34 | Srivastava A\*, Malik L, Smith T, Sudbery I, Patro R. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Keywords: dscRNA-seq, Quantification, UMI-Deduplication, salmon, alevin. 35 | 36 | 37 | Barrows D\*, Allis CD, Carroll T. Visualization and annotation of read signal over genomic ranges with profileplyr. Keywords: ChIPSeq, ChipOnChip, Coverage, DataImport, Sequencing. 38 | 39 | 40 | Eliatan Niktab\*, Dinindu S Senanayake, Andrew B Munkacsi, Paul H Atkinson, Kelly V. Ruggles, Mark Walterfang. Title TBD. Keywords: GraphAndNetwork, GenomeWideAssociation, AnnotationData, SNPData. 41 | 42 | Odom G\*, Ban Y\*, Liu L, Wang L, Chen X. Integrative pathway analysis with modern PCA methodology and gene selection. Keywords: Pathways, GeneSetEnrichment, DimensionReduction, FeatureExtraction, PrincipalComponent. 43 | 44 | Eric Bouillet, Christine Choirat\*, Rok Roskar, Chandrasekhar Ramakrishnan, Olivier Verscheure, and the RENKU development team. Reproducible workflows and Bionconductor package development with the RENKU platform. Keywords: Reproducibility, Common Workflow Language, Continuous Integration, Docker. 45 | 46 | Ward C, To TH, Pederson S\*. ngsReports and strandCheckR: Two QC packages for bolting directly into NGS pipelines. Keywords: QualityControl, ReportWriting. 47 | 48 | Burton D\*, McCall MN. Likelihood Based Mixture Modeling in Gene Regulatory Network Inference. Keywords: NetworkInference, SystemsBiology, GeneRegulation, GeneExpression, CancerData. 49 | 50 | Zhu A\*, Srivastava A, Ibrahim J, Patro R, and Love M. Nonparametric method for Differential Analysis of RNA-Seq with Quantification Uncertainty. Keywords: GeneExpression, RNAseq, Sequencing, GeneExpression, DifferentialExpression. 51 | 52 | 53 | ### Session 2 - __Group B - 5:30 to 7:30 (26th June) in Weiss lobby__ 54 | 55 | 56 | Robert A. Amezquita\*, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L.Lun, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Mike Smith, Wolfgang Huber, Hervé Pagès, Martin Morgan, Raphael Gottardo, and Stephanie C. Hicks. Orchestrating Single-Cell Analysis with Bioconductor. Keywords: scRNAseq, singlecell, genomics, review. 57 | 58 | Farias Amorim C\*, Berry A, Beiting DP. Title TBD. Keywords: Parasite, Host, RNAseq, Transcriptomics, Infectious Diseases. 59 | 60 | Sonali Arora\*, Siobhan Pattwell, Eric Holland, Hamid Bolouri. Gene specific variability between commonly used RNA-seq pipelines. Keywords: TCGA, GTEx, rna-seq, big-data, genomics. 61 | 62 | Avshalumov A\*, Rahman M\*, Wultsch C, and Krampis K. MicrobiomeExplorer: An interactive and web-based R Shiny analysis platform for microbiome research. Keywords: Microbiome, Metagenomics, Clustering, Visualization, Software. 63 | 64 | Belleau P\*, Deschenes A\*, Adelaja A, Medina S, Ranade N, and Dillman A. HLAClusteRView: HLA typing clustering and visualization based on specific similarity metrics. Keywords: Visualization, Software, ImmunoOncology, Clustering, BiologicalQuestion. 65 | 66 | Brehm Z\*, Halushka M and McCall M. Deconvolutional mixture modeling to account for cell-type composition in tissue samples. Keywords: RNASeq, GeneExpression. 67 | 68 | Antonio Colaprico\*, Catharina Olsen, Claudia Cava, Thilde Terkelsen, Matthew H. Bailey, Tiago C. Silva, André Vidas Olsen, Laura Cantini, Andrei Zinovyev, Emmanuel Barillot, Gloria Bertoli, Isabella Castiglioni, Houtan Noushmehr, Gabriel J. Odom, Xi Chen, Gianluca Bontempi, Elena Papaleo. Title TBD. Keywords: DNAMethylation, GeneExpression, Pathways, Sequencing, Software. 69 | 70 | Dragich J\*. A BioC workflow to go from high-throughput genetic data back to detailed, personalized genetic insights. Keywords: Genetic, variant, human, haploinsufficient, protein. 71 | 72 | Jessica R. Holmes, Jenny Drnevich\*, Lois L. Hoyer, Christopher J. Fields. Broadening the impact of bioinformatics in research and education. Keywords: RNASeq. 73 | 74 | Huang D\*, Coban EB, Wultsch C, Liu J, Casaccia P, Krampis K. Noise filtering, exploratory data analysis and trajectory inference from single-cell (scSeq) genomic sequencing using the R / Bioconductor software libraries. Keywords: SingleCellWorkflow, SingleCell, Transcriptomics, Visualization, BiomedicalInformatics. 75 | 76 | Nahed Jalloul\*, Greg Reidlinger, Shridar Ganesan, Hossein Khiabanian. Title TBD. Keywords: targeted sequencing panels, bioinformatics analysis, clinical implementation. 77 | 78 | Lawson J\*, Smith J, Garrett-Bakelman F, Bekiranov S, and Sheffield N. Coordinate Covariation Analysis (COCOA): Understanding Interindividual Variation in Data with Genomic Coordinates. Keywords: Epigenetics, GenomeAnnotation, GenomicVariation, PrincipalComponent. 79 | 80 | Loh JW\*, Guccione C, Di Clemente F, Riedlinger G, Ganesan S, and Khiabanian H. All-FIT: Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data. Keywords: clinical sequencing, specimen purity estimation, tumor-only sequencing. 81 | 82 | Martin, T.C.\*, Bell, J.T. coMET: visualization of regional epigenome-wide association scan results and DNA co-methylation patterns. Keywords: Visualization, ChIPSeq, DNAMethylation, GenomeWideAssociation, MethylSeq. 83 | 84 | Gu Y, McDavid A\*. CellaRepertorium Facilitates scRNAseq Immune Repertoire Analysis. Keywords: SingleCell, ImmunoOncology, Sequencing, QualityControl, MultipleComparison. 85 | 86 | Hatice U. Osmanbeyoglu\*, Fumiko Shimizu, Angela Rynne-Vidal, Direna Alonso-Curbelo, Hsuan-An Chen, Hannah Y. Wen, Tsz-Lun Yeung, Petar Jelinic, Pedram Razavi, Scott W. Lowe, Samuel C. Mok, Gabriela Chiosis, Douglas A. Levine, Christina S. Leslie. Title TBD. Keywords: software. 87 | 88 | Ploenzke MS\*, Irizarry RI. Shallow convolutional methods for learning genomic sequence motifs. Keywords: convolution neural network motif interpretable. 89 | 90 | Anna Quaglieri\*, Christoffer Flensburg. Varikondo: spark joy in your variants!. Keywords: DataImport, Sequencing, GeneticVariants, Tidy, Standardise. 91 | 92 | 93 | Sanjeev Sariya\* and Giuseppe Tosto. Epistasis analysis for Late-Onset of Alzheimer’s disease (LOAD) using Exome-Chip data. Keywords: Epistasis, interaction, exome. 94 | 95 | Hirak Sarkar\*, Avi Srivastava and Rob Patro. Minnow: A principled framework for rapid simulation of dscRNA-seq data at the read level. Keywords: scRNA-seq, simulation, multi mapping. 96 | 97 | Singh A\*, Bhanot G, Khiabanian H. TuBA: Tunable Biclustering Algorithm for uncovering altered transcriptional profiles in large gene expression datasets of tumors. Keywords: Transcriptomics, biclustering, gene co-expression, tumor heterogeneity. 98 | 99 | Singh R\*, Ramzan T\*, Avshalumov A, Rahman M, Wultsch C, Krampis K. Human microbiome and minority health: unravelling variations associated with disease and ethnicity. Keywords: Microbiome, MultipleComparison, Metagenomics, BiomedicalInformatics. 100 | 101 | Elitsa Stoyanova\*, Eric Schmidt, Thomas Carroll, Nathaniel Heintz. trapr And trapr.db: A software package for the curation, assessment and visualization of trap-seq data. Keywords: RNASeq, GeneExpression. 102 | 103 | A. B. Villaseñor-Altamirano\*, Y. I. Balderas-Martínez, M. Moretto, A. Zayas-Del Moral, M. Maldonado, A. Munguía-Reyes, J. S. García-Sotelo, L. A. Aguilar Bautista, K. Engelen, M. Selman, A. Medina-Rivera, J. Collado-Vides. Title TBD. Keywords: None Given. 104 | 105 | 106 | 107 | 108 | 109 | -------------------------------------------------------------------------------- /docs/code_of_conduct.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | 5 | # BioC2019 Code of Conduct violation response 6 | 7 | [Traducción al español][1] 8 | 9 | This statement is in response to a complaint of sexual harassment made to the BioC2019 [Code of Conduct committee][0] after the BioC2019 conference. A BioC2019 conference attendee reported unwelcome sexual attention and inappropriate physical contact from an intoxicated conference attendee, during a social gathering of conference attendees. Since the time when the complaint was made the Committee has followed up with the complainant, the accused, and others present, and sought external advice from persons outside the organization to define procedures to make appropriate decisions to deal with this and future reports of violation of the code of conduct. The committee decided on the following actions: 10 | 11 | * The accused will be ineligible to attend Bioconductor conferences for three years following the event (specifically BioC2020, BioC2021, BioC2022). 12 | * In order to attend future Bioconductor conferences after this period, the accused must make a written request to the BioC Code of Conduct Committee. If the Committee unanimously agrees that the accused no longer presents an elevated risk of future Code of Conduct violations, the accused will again be permitted to attend Bioconductor conferences. 13 | * The accused will be ineligible for future financial support from the Bioconductor organization. 14 | 15 | The Code of Conduct Committee undertook these actions with the goal of maintaining a welcoming and harassment-free environment at future conferences. With this goal in mind, we wish to remind all participants that: 16 | 17 | * Bioconductor does not tolerate harassment, intimidation, or bullying of conference participants in talks, workshops, poster sessions, social activities, or online. This includes informal gatherings of conference participants outside of formally scheduled activities. 18 | * Sexual attention does not have to be explicitly lewd in order to violate the Code of Conduct, which states simply that unwelcome sexual attention or inappropriate physical contact is harassment. 19 | * Drunkenness is not an excuse for committing a Code of Conduct violation. Neither is unfamiliarity with the Code of Conduct. 20 | * All conference participants are responsible for treating others in a professional and respectful manner within the bounds of our Code of Conduct. Anyone violating the Code of Conduct, from first-time attendees to senior leaders, will be held accountable. 21 | 22 | People generally participate in Bioconductor conferences for professional or academic interest, and expect to interact with colleagues on the primary basis of shared interests in open-source Bioinformatics. Unwanted sexual attention, and other actions forbidden by the [Code of Conduct][2], deny others of this experience. The Code of Conduct committee encourages all conference participants to review the Code of Conduct and to enjoy their time at the conference while remembering their responsibility to maintain a supportive, collegial, and harassment-free conference experience for everyone. Anyone experiencing or witnessing a Code of Conduct violation should report it either to [code-of-conduct@bioconductor.org][0], a member of the Code of Conduct committee, or anonymously at [https://tinyurl.com/bioccomplaint](https://tinyurl.com/bioccomplaint). 23 | 24 | This complaint was handled by the Bioconductor Code of Conduct Committee (Levi Waldron, Aedin Culhane, Laurent Gatto, Stephanie Hicks) and this response was approved by the [Bioconductor Technical Advisory Board][3]. 25 | 26 | # BioC2019 Code of Conduct 27 | 28 | ## Social media policy 29 | 30 | Images and content from talks, workshops, and posters may be shared publicly through social media _unless_ the presenter asks for it not to be. To avoid confusion, presentations not to be shared should be labeled "Do Not Share" on each slide, as should be posters. 31 | 32 | ## The _Bioconductor_ conference aims to provide a supportive, collegial, and harassment-free environment 33 | 34 | _Bioconductor_ is dedicated to providing a supportive, collegial, and harassment-free 35 | conference experience for everyone, regardless of: 36 | * gender, gender identity and expression, sexual orientation, disability, 37 | physical appearance, body size, race, age or religion. 38 | * intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc. 39 | 40 | We do not tolerate harassment, intimidation, or bullying of conference participants in talks, 41 | workshops, poster sessions, social activities, 42 | or online. Sexual language and imagery is not appropriate for any conference venue, including talks. 43 | Conference participants violating these rules may be sanctioned or expelled from the conference with no refund, 44 | at the discretion of the conference organizers. Our anti-harassment policy can be found at: [http://bioc2019.bioconductor.org/code_of_conduct] 45 | 46 | ## Examples of unacceptable harassment, intimidation, and bullying behavior 47 | 48 | Harassment includes, but is not limited to: 49 | 50 | * Making comments, to an audience or personally, that belittle or demean another person 51 | * Sexual images in public spaces 52 | * Stalking or following 53 | * Harassing photography or recording 54 | * Sustained disruption of talks or other events 55 | * Inappropriate physical contact 56 | * Unwelcome sexual attention 57 | * Advocating for, or encouraging, any of the above behaviour 58 | 59 | Intimidation and bullying include, but are not limited to: 60 | 61 | * Aggressive or browbeating behavior directed at someone during a public presentation 62 | * Mocking or insulting another person's intellect, work, perspective, or question/comment 63 | * Making reference to someone's gender, gender identity and expression, sexual orientation, disability, 64 | physical appearance, body size, race, age, religion, or other personal attribute in the context of a scientific 65 | discussion 66 | * Deliberately making someone feel unwelcome 67 | 68 | ### Enforcement 69 | 70 | Participants asked to stop any harassing behavior are expected to comply immediately. 71 | 72 | If a participant engages in harassing behaviour, event organisers retain the right to take any actions to keep the event a welcoming environment for all participants. This includes warning the offender or expulsion from the conference with no refund. 73 | 74 | Event organisers may take action to redress anything designed to, or with the clear impact of, disrupting the event or making the environment hostile for any participants. 75 | 76 | We expect participants to follow these rules at all event venues and event-related social activities. We think people should follow these rules outside event activities too! 77 | 78 | ### Reporting 79 | 80 | If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible. 81 | Harassment and other code of conduct violations reduce the value of our event for everyone. 82 | We want you to be happy at our event. People like you make our event a better place. 83 | 84 | You can make a report either personally or anonymously. 85 | 86 | #### Anonymous or Non-anonymous Report 87 | 88 | You can make an anonymous or non-anonymous report here: [https://tinyurl.com/bioccomplaint]. It is a free-form text box that will be forwarded to conference organizers. 89 | 90 | We can't follow up an anonymous report with you directly, but we will fully investigate it and take whatever action is necessary to prevent a recurrence. 91 | 92 | #### Personal Report 93 | 94 | You can make a personal report with any of the conference anti-harassment committee: Aedin Culhane, Levi Waldron, and Laurent Gatto. 95 | 96 | When taking a personal report, our staff will ensure you are safe and cannot be overheard. They may involve other event staff to ensure your report is managed properly. Once safe, we'll ask you to tell us about what happened. This can be upsetting, but we'll handle it as respectfully as possible, and you can bring someone to support you. You won't be asked to confront anyone and we won't tell anyone who you are. 97 | 98 | Our team will be happy to help you contact hotel/venue security, local law enforcement, local support services, provide escorts, or otherwise assist you to feel safe for the duration of the event. We value your attendance. 99 | 100 | Conference organizers: workshop@bioconductor.org 101 | Anonymous complaints: tinyurl.com/bioccomplaint 102 | Local law enforcement: 911 103 | Local sexual assault hot line: 212-227-3000 104 | 105 | | Photo | Name | 106 | |---|---|---| 107 | | | Aedin Culhane <[aedin@jimmy.harvard.edu][4]> | 108 | | | Levi Waldron <[lwaldron.research@gmail.com][5]> | 109 | | | Laurent Gatto <[laurent.gatto@uclouvain.be][6]> | 110 | 111 | [0]: mailto:code-of-conduct@bioconductor.org 112 | [1]: https://comunidadbioinfo.github.io/es/post/bioc2019-code-of-conduct-violation-response 113 | [2]: https://bioc2019.bioconductor.org/code_of_conduct 114 | [3]: https://www.bioconductor.org/about/technical-advisory-board/ 115 | [4]: mailto:aedin@jimmy.harvard.edu?subject=BioC2019%20code-of-conduct 116 | [5]: mailto:lwaldron.research@gmail.com?subject=BioC2019%20Code-of-conduct 117 | [6]: mailto:laurent.gatto@uclouvain.be?subject=BioC2019%20Code-of-conduct 118 | -------------------------------------------------------------------------------- /docs/assets/css/style.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Noto Sans'; 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} 441 | 442 | header li, header ul li + li + li { 443 | width: 33%; } } 444 | @media print { 445 | body { 446 | padding: 0.4in; 447 | font-size: 12pt; 448 | color: #444; } } 449 | -------------------------------------------------------------------------------- /docs/travel-accommodations.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | 5 | # BioC 2019: Where Software and Biology Connect 6 | 7 | When: June 24 - 27, 2019
8 | What: Developer Day, Main Conference, Symposium
9 | Where: [NYU and Rockefeller University][venue], New York City, USA
10 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
11 | Twitter: [#bioc2019][tweet]
12 | 13 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 14 | [venue]: ./travel-accommodations 15 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 16 | 17 | ## Venue 18 | 19 | The conference will take place in two venues: 20 | - Developer Day (June 24) at NYU Langone School of Medicine ([1st 21 | Avenue and East 30th Street](https://goo.gl/maps/WbtSVCpnrR92)) 22 | - Main Conference and Robert Gentleman Symposium (June 25-27) at 23 | Rockefeller University ([York Avenue and East 66th 24 | Street](https://goo.gl/maps/JkRcufXyhrq)). 25 | 26 | ## Accomodations 27 | 28 | The conference venues are most easily accessible from the east side of Manhattan (especially around Grand Central Terminal) and from Long Island City (LIC). LIC provides good value for the price, but will require taking the subway (or a cablecar over the East River if you are near the bridge to Roosevelt Island!) 29 | 30 | The following link may provide group rate discounts for hotels close to the venues: [https://groups.hotels.com/093853217/EventPage4975917](https://groups.hotels.com/093853217/EventPage4975917) 31 | 32 | ### Most affordable options 33 | 34 | Long Island City (LIC) provides affordable hotel options (starting at ~$120/night+14.75% tax), and is 25-30 minutes by transit to both Rockefeller University and NYU Langone Medicine. 35 | 36 | * [Days Inn by Windham LIC](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=18518&idTypeId=0&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gid=4975917#HotelName) (starting at $118+tax) 37 | * [Best Western Plus Plaza Hotel LIC](https://groups.hotels.com/eh/2ynfx-5avp) (starting at $121+tax) 38 | * [Voyage Hotel LIC](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=1025803&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (starting at $126+tax) 39 | * [Mayflower Boutique Hotel](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=764861&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (starting at $97+tax) 40 | * [Red Lion Inn & Suites LIC](https://groups.hotels.com/eh/2ynfx-5tsn) (starting at $157+tax) 41 | * [Queens Count Inn & Suites LIC](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=802430&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (starting at $119+tax) 42 | * [Holiday Inn LIC](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=38080&idTypeId=0&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gid=4975917#HotelName) (starting at $155+tax) 43 | 44 | ### Most convenient options 45 | 46 | These options are easy walking distance from Rockefeller University, but are > $250 / night. 47 | 48 | * [The Bentley hotel](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=143951&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (6 minute walk to RU, starting at $240+tax) 49 | * [The Lombardy Hotel](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=122563&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (20 minute walk to RU, 34 minutes walk to NYU, close to 6 train for going to NYU, starting at $272+tax) 50 | 51 | Closer to NYU: 52 | 53 | * [The Lexington Hotel](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=109730&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (starting at $213+tax) 54 | * [The Roger Smith Hotel](https://groups.hotels.com/Hotel/HotelRoomTypes.htm?hotelID=179766&inDate=06/23/19&outDate=06/27/19&NumRooms=1&gp=78.00&gid=4975917#HotelName) (starting at $211+tax) 55 | 56 | ## NYU Langone 57 | 58 | Please arrive at NYU through the main entrance on 1st Avenue between 59 | 30th and 34th street. 60 | 61 | 62 | 63 | ### Local Transportation to NYU 64 | 65 | **Buses**: The M15 local bus runs the length of First Avenue in 66 | Manhattan and stops near the front of the NYU Langone Medical 67 | Center. For the M15 limited bus, which runs express, the closest stop 68 | is at 29th Street. The M34 bus runs the length of 34th Street in 69 | Manhattan and stops directly in front of the north entrance to NYU 70 | Medical Center on 34th Street at First Avenue. The M16 bus, which 71 | connects with nationwide bus service at the Port Authority Bus 72 | Terminal (42nd Street and Eighth Avenue), has a nearby stop at First 73 | Avenue and 23rd Street. One bus fare is $2.50. A MetroCard or coins 74 | are required. 75 | 76 | **Subway**: The subway costs $2.75. The stops closest to the NYU 77 | Langone Medical Center and the Bellevue Hospital Center are: 33rd 78 | Street or 28th Street stops (at Park Avenue) on the Number 6 line. 79 | Grand Central Terminal at 42nd Street between Lexington Avenue and 80 | Park Avenue (4, 5, 6). 81 | 82 | **Available Parking Options**: 83 | https://nyulangone.org/locations/tisch-hospital/parking 84 | 85 | ### Getting around NYU Langone 86 | 87 | **Farkas Auditorium**: Follow the Yellow Pathway and you will quickly 88 | come upon the Alumni Hall. The Farkas Auditorium will be to your 89 | right. If you have reached the Medical Science Building then you have 90 | gone too far. Registration will take place here. Smilow Research 91 | Center—Found at the very end of the Yellow Pathway. Upon entering the 92 | Medical Center, take the Yellow Pathway to the Smilow elevator bank at 93 | the back of the building. 94 | 95 | **Medical Science Building (MSB)**: Found midway along the Yellow 96 | Pathway. The MSB conference room for the workshop can be found down 97 | by continuing past the elevators into the Smilow Research Building and 98 | continuing down the stairs (or taking the elevator 1 floor down). 99 | 100 | **Science Building (SB)**: The main entrance of this building is 101 | located on E. 30th Street and has access points from the Smilow 102 | Research Center and the Medical Science Building. From MSB, please 103 | take the elevators to the ground floor and follow the signs marked 104 | “Science Building.” This building can also be access by a bridge next 105 | to the Smilow Seminar Room. 106 | 107 | 108 | ## Rockefeller University 109 | 110 | ### Arrival at Rockefeller. 111 | 112 | Please arrive to Rockefeller at the entrance on 66th street and York avenue. 113 | 114 | 115 | 116 | ### Local transportation to Rockefeller University 117 | 118 | **Buses**: Two buses stop near the main entrance: the York Avenue/ 119 | 57th Street crosstown ([M31](https://goo.gl/maps/4B6XGsNuutN2)) and 120 | the 68th Street crosstown ([M66](https://goo.gl/maps/65d1PmCWNLo)) 121 | ([Metropolitan Transit 122 | Authority](http://web.mta.info/nyct/maps/manbus.pdf)). Both routes 123 | pass within steps of the entrance. 124 | 125 | **Subway**: Take the 6 to the [68th Street/Hunter 126 | College](https://goo.gl/maps/Xz6Yw3vBKF22) and walk east or the Q to 127 | [2nd Avenue/72nd Street](https://goo.gl/maps/rjLdxUPD2KA2) and exit at 128 | 69th street. Rockefeller is half a mile from the Subway. 129 | 130 | **Tramway (cable car)**: The Manhattan stop of the [Roosevelt Island 131 | Tramway](https://en.wikipedia.org/wiki/Roosevelt_Island_Tramway) is a 132 | 7 minute walk from Rockefeller University. This is likely to take a 133 | little extra time but can be a nice option if you are staying along 134 | the F line or within walking distance of the [Roosevelt Island F line 135 | subway station](https://goo.gl/maps/XGmuQrFgzA82) in Long Island 136 | City. The tramway uses the Metrocard and costs a regular subway fare. 137 | 138 | **Taxis** [estimated 139 | costs](https://www.taxifarefinder.com/main.php?city=NY&lang=en). 140 | 141 | **Bicycle racks** are at the end of 68th Street parking lot under the 142 | tennis court by the staircase in the back. 143 | 144 | ### Arriving by air 145 | 146 | The main airports that serve New York City are 147 | [LGA](https://www.laguardiaairport.com/), 148 | [JFK](https://www.jfkairport.com/), and 149 | [EWR](https://www.newarkairport.com/) (Newark). 150 | 151 | #### Arriving to Manhattan from JFK. 152 | 153 | * **Taxi** - Taxis from JFK offer a flat rate of $50-$70 to Manhattan 154 | (not including tips or tolls). Taxi rank can be found directly 155 | opposite departure's entrance. [JFK taxi 156 | information](https://www.airport-jfk.com/taxi.php) 157 | * **Public Transport** - JFK airtrain tickets cost $7.75 and connects 158 | JFK station to Penn station W.34 street with free transfer to the 159 | MTA subway system in Manhattan. [JFK airtrain 160 | information](https://www.airport-jfk.com/airtrain.php). 161 | 162 | #### Arriving to Manhattan from Newark. 163 | 164 | * **Taxi** - Meatured taxi services are available at Newark. Taxi 165 | rates will vary due to rush hour traffic, typically ranging from 166 | $60~$110. [Newark taxi 167 | information](https://www.newarkairport.com/to-from-airport/taxi-car-and-van-service). 168 | * **Public Transport** - Newark airtrain connects from airport to New 169 | York Penn Station in around 30-45 minutes with tickets approximately 170 | $12.50.[Newark airtrain 171 | information](https://www.newarkairport.com/to-from-airport/air-train). 172 | 173 | #### Arriving to Manhattan from LaGuardia. 174 | 175 | * **Taxi** - Meatured taxi services are available at LaGuardia. Taxi 176 | rates will vary due to rush hour traffic, typically ranging from 177 | $40~$60 for LaGuardia. [LaGuardia taxi 178 | information](https://www.laguardiaairport.com/to-from-airport/by-taxi). 179 | * **Public Transport** - MTA buses run from LaGuardia to Manhattan and 180 | cost roughly $2.75 for a one-way ticket. [LaGuardia MTA buses 181 | information](https://www.laguardiaairport.com/to-from-airport/public-transportation). 182 | 183 | 184 | ### Driving and parking 185 | 186 | Take the FDR Drive southbound to 63rd Street or northbound to 61st Street; 187 | turn right on York Avenue. 188 | There is no parking on campus. Here are the closest places to park: 189 | 190 | - Greenberg Garage 191 | at New York-Presbyterian Hospital at 192 | [525 E. 68th Street](https://goo.gl/maps/Xo5wQDCsPKR2) 193 | (entrance at 68th Street, east of York Avenue). 194 | - Quick Park / SP+ Parking at 195 | [450 E. 63rd Street](https://goo.gl/maps/5VdxzpJ285A2) 196 | (between York and 1st Avenue). 197 | -------------------------------------------------------------------------------- /docs/talks-community.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: default 3 | --- 4 | # BioC 2019: Where Software and Biology Connect 5 | 6 | When: June 24 - 27, 2019
7 | What: Developer Day, Main Conference, Symposium
8 | Where: [NYU and Rockefeller University][venue], New York City, USA
9 | Slack: [Bioconductor Team][] (`#bioc2019` channel)
10 | Twitter: [#bioc2019][tweet]
11 | 12 | [tweet]: https://twitter.com/hashtag/bioc2019?f=tweets 13 | [venue]: ./travel-accommodations 14 | [Bioconductor Team]: https://bioc-community.herokuapp.com/ 15 | 16 | ## Community-Contributed Talks (Tentative) 17 | 18 | - See the Conference [Schedule](schedule.md) for invited talks. 19 | 20 | - Lee S\*, Cook D, Lawrence M. _[plyranges][]: a fluent interface to 21 | Bioconductor's Ranges infrastructure_. The Bioconductor project has 22 | created many powerful S4 classes for reasoning about genomics data, 23 | such as the SummarizedExperiment class for representing experimental 24 | assays and the Ranges family of classes for representing genomic 25 | intervals. For new users of Bioconductor who are unfamiliar with 26 | object oriented programming or genomic data analysis, the learning 27 | curve for these classes is steep. New users often find themselves 28 | asking: how do I get my data into an appropriate class for my 29 | analysis? What are accessors and why do I have to use them? Why does 30 | this function return an object of class that I have not seen before? 31 | This results in analysts trying to solve problems that have been 32 | efficiently dealt with in other Bioconductor packages or writing 33 | code they may not fully understand. 34 | 35 | The goal of a fluent interface is to enable users to write 36 | human-readable code via method chaining and consistent function 37 | returns. Fluent interfaces fit naturally in the context of 38 | Bioinformatics workflows because they enable writing succinct 39 | pipelines. We have developed plyranges a package that attempts to 40 | construct a fluent interface to the Ranges classes defined in the 41 | IRanges and [GenomicRanges][] packages. This package is inspired by 42 | [dplyr][] and implements and extends its grammar of data 43 | manipulation to Ranges. We have defined methods for constructing, 44 | grouping, mutating, filtering, and summarising Ranges. We have also 45 | defined an algebra for reasoning about actions on Ranges and 46 | relationships between Ranges. By having an expansive grammar, we 47 | hope to cover the majority of analysis tasks a new user may face and 48 | thereby enable users to write clearer and more reproducible code. 49 | 50 | - Zhun Miao\*, Ke Deng, Xiaowo Wang, Xuegong Zhang. _[DEsingle][] for 51 | detecting three types of differential expression in single-cell 52 | RNA-seq data_. The excessive amount of zeros in single-cell RNA-seq 53 | (scRNA-seq) data includes ‘real’ zeros due to the on-off nature of 54 | gene transcription in single cells and ‘dropout’ zeros due to 55 | technical reasons. Existing differential expression (DE) analysis 56 | methods cannot distinguish these two types of zeros. 57 | 58 | We developed an R package [DEsingle][] which employed Zero-Inflated 59 | Negative Binomial model to estimate the proportion of real and 60 | dropout zeros and to define and detect three types of DE genes in 61 | scRNA-seq data, with regard to different expression status (DEs), 62 | differential expression abundance (DEa), and general differential 63 | expression (DEg). 64 | 65 | Results showed that [DEsingle][] outperforms existing methods for 66 | scRNA-seq DE analysis, and can reveal different types of DE genes 67 | that are enriched in different biological functions. 68 | 69 | - Abbas Rizvi\*, Ezgi Karaesmen\*, Leah Preus, Michael Sovic, Junke 70 | Wang, Lara Sucheston-Campbell. _[gwasurvivr][]: an R package to 71 | perform survival association testing on imputed genetic data_. 72 | Increasingly researchers have become interested in time-to-event 73 | outcomes in the context of genetic variation. Existing software for 74 | performing survival analyses across millions of SNPs are 75 | limited. Recently, comprehensive stand-alone software packages, 76 | genipe and SurvivalGWAS_SV, were developed, however, they require 77 | user interaction with the raw output after imputation opening room 78 | for error during analysis. GWASTools, while available in R and can 79 | implement survival, is primarily for storing large SNP datasets and 80 | rigorous QC/QA. To address this unmet need, we developed an 81 | R/Bioconductor package to conduct fast and efficient genome wide 82 | survival analyses for on imputed genetic data generated using 83 | IMPUTE2 and VCF data generated from Michigan or Sanger imputation 84 | servers. 85 | 86 | [gwasurvivr][] implements Cox proportional hazards models to test 87 | SNP association with outcome; the package allows for covariates and 88 | SNP-covariate interaction. To potentially decrease the number of 89 | iterations needed for convergence when optimizing the parameters 90 | estimates in the Cox model, we modified survival::coxph.fit, to fit 91 | covariates without the SNP and use those parameter estimates as 92 | initial starting points. For models without covariates the parameter 93 | estimation optimization begins with null initial value. Users can 94 | internally subset the data by providing sample IDs and pre-filter 95 | SNPs by info score and MAF. Output for each SNP includes parameter 96 | estimates, p-values, MAFs, INFO scores, number of events and total 97 | sample N. [gwasurvivr][] is well-suited for multi-core processors 98 | and users can specify node preferences used during computation. To 99 | overcome R memory limitations [gwasurvivr][] iteratively performs 100 | survival on subsets of the entire data. 101 | 102 | We benchmarked our package with genipe, SurvivalGWAS_SV, and 103 | GWASTools using IMPUTE2 data for varying sample sizes (n=100, 104 | n=1000, n=5000) and SNPs (p=1000, p=10000, p=100000) including two 105 | non-genetic covariates. All packages showed excellent agreement 106 | across MAF estimates, coefficient estimates, and p-values, with 107 | [gwasurvivr][] outperforming the other packages in time to 108 | completion for all simulations. 109 | 110 | - Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Lucas Schiffer, 111 | Marcel Ramos, Ralf Zimmer, and Levi Waldron. _Towards a gold 112 | standard for benchmarking gene set enrichment analysis._ Although 113 | gene set enrichment analysis has become an integral part of 114 | high-throughput gene expression data analysis, the assessment of 115 | enrichment methods remains rudimentary and ad hoc. In the absence of 116 | suitable gold standards, the evaluation is commonly restricted to 117 | selected data sets and biological reasoning on the relevance of 118 | resulting enriched gene sets. However, this is typically incomplete 119 | and biased towards the individual investigation goals. In this 120 | article, we present a curated compendium of 50 expression data sets 121 | investigating 34 different human diseases. The compendium features 122 | microarray and RNA-seq measurements, and each data set is associated 123 | with a precompiled GO/KEGG relevance ranking for the corresponding 124 | disease under investigation. We perform a comprehensive assessment 125 | of 20 major enrichment methods based on the benchmark set, thereby 126 | identifying methods that accurately recover the a priori defined 127 | relevance rankings. The compendium is embedded in a directly 128 | executable benchmark system, the _R / Bioconductor_ 129 | [GSEABenchmarkeR][] package, allowing straightforward execution on 130 | additional enrichment methods. 131 | 132 | - Nima Hejazi\*, Alan Hubbard, Mark van der Laan. _Data-Adaptive 133 | Estimation and Inference for Differential Methylation Analysis_. DNA 134 | methylation is amongst the best studied of epigenetic mechanisms 135 | impacting gene expression. While much attention has been paid to the 136 | proper normalization of bioinformatical data produced by DNA 137 | methylation assays, linear models remain the current standard for 138 | analyzing post-processed methylation data, for the ease they afford 139 | for both statistical inference and scientific interpretation. We 140 | present a new, general statistical algorithm for the model-free 141 | estimation of the differential methylation of DNA CpG sites, 142 | complete with straightforward and interpretable statistical 143 | inference for such estimates. The new approach leverages variable 144 | importance measures, a class of parameters arising in causal 145 | inference, in a manner that facilitates their use in obtaining 146 | targeted estimates of the importance of each CpG site. The proposed 147 | procedure is computationally efficient and self-contained, 148 | incorporating techniques to isolate a subset of candidate CpG sites 149 | based on cursory evidence of differential methylation and providing 150 | a multiple testing correction that appropriately controls the False 151 | Discovery Rate in such multi-stage analysis settings. The 152 | effectiveness of the new methodology is demonstrated by way of data 153 | analysis with real DNA methylation data, and a recently developed R 154 | package (methyvim; available via Bioconductor) that provides support 155 | for data analysis with this methodology is introduced. 156 | 157 | - Albert Y Zhang, Shian Su, Matthew E Ritchie, and Charity W 158 | Law\*. _Unpacking signal from RNA-seq intron reads using Rsubread and 159 | limma packages_. RNA-seq datasets contain up to millions of intron 160 | reads per library. These reads are typically removed from downstream 161 | analysis without even considering the proportion at which they 162 | contribute to total reads. By default only reads overlapping 163 | annotated exons are thought to be informative since mature mRNA is 164 | assumed to be the major component sequenced, especially when 165 | examining poly(A) RNA samples. Using Bioconductor packages, Rsubread 166 | and limma, we show that intron reads contain signal that is 167 | biologically relevant. Multi-dimensional scaling plots show that 168 | samples separate into biological and experimental groups using 169 | conservative intron counts, where the degree of separation is 170 | similar to that of exon counts despite there being far fewer intron 171 | reads in comparison to exon reads. The coverage of exon and intron 172 | regions are assessed for thousands of genes, showing a tendency for 173 | an increase in read coverage from 3' to 5' in poly(A) RNA 174 | samples. Coverage in Total RNA samples tend to be more uniform in 175 | appearance. We show that intron signal is prevalent across multiple 176 | datasets and discuss the possibility of its origin from pre-mRNA and 177 | intron retention. Results presented here can be used in the 178 | development of future Bioconductor packages to interrogate different 179 | biological aspects relating to intron signal, and inspire 180 | modifications to existing methods for RNA-seq analysis. 181 | 182 | - Rachael V Phillips\*, Alan Hubbard. _Data Adaptive Evaluation of 183 | Preprocessing Methods using Ensemble Machine Learning_. For many 184 | types of biological data generated by high-throughput technologies, 185 | there is no single gold-standard for converting the raw data into a 186 | form that can be analyzed for relationships of the relevant 187 | biomarkers to exposures and disease. For example, much of the 188 | variation in the raw data generated by Illumina HumanMethylationEPIC 189 | and 450K arrays is due to the technicalities of the experimental 190 | design (comprising two different assay methods, two different color 191 | channels, and batch effects) and potentially less so due to the 192 | biological factor(s) of interest. Accordingly, several preprocessing 193 | methods have been developed, however it is unclear which combination 194 | should be retained in downstream analysis. To address this issue, we 195 | have developed a data adaptive methodology that incorporates 196 | ensemble machine learning to assess which preprocessing streams 197 | generate better signal-to-noise ratio, according to the prediction 198 | of positive and negative control variables. We employ this method to 199 | select normalizations for EPIC and 450K arrays in a principled 200 | way. The results suggest 1) differences in the relative performance 201 | of the possible preprocessing choices and 2) that such machine 202 | learning approaches can be practically applied to complex omics data 203 | to choose among the growing number of choices for preprocessing. 204 | 205 | - Steinbaugh MJ\*, Kirchner RD, Ho Sui S. _bcbioSingleCell: R package 206 | for bcbio single-cell analysis_. Single-cell RNA sequencing 207 | (scRNA-seq) has ushered in a new era of genomics research, enabling 208 | researchers to visualize dynamic changes in cell populations, and 209 | quantify changes in gene expression at an unprecedented new level of 210 | resolution. While this new technology is extremely exciting and 211 | empowering, it remains overly challenging for the vast majority of 212 | biologists to import and analyze their results with confidence. The 213 | bcbio toolkit addresses this problem, offering native best-practice 214 | support for quantification of multiple barcoded droplet platforms, 215 | including inDrops, Drop-seq, 10X Genomics Chromium, and Illumina 216 | SureCell. The corresponding R package, _bcbioSingleCell_, provides 217 | support for easy loading of results into the SingleCellExperiment 218 | container class. Using the standardized SingleCellExperiment 219 | container enables researchers to efficiently pass their data to 220 | other single-cell packages available on Bioconductor. Additionally, 221 | the package offers a suite of quality control functions optimized 222 | for low quality cellular barcode removal, along with clustering and 223 | visualization functions that integrate with the Seurat 224 | toolkit. Differential expression analysis is supported and utilizes 225 | the zero-inflated negative binomial model provided by zinbwave, thus 226 | unlocking downstream testing with the robust DESeq2 or edgeR RNA-seq 227 | packages. 228 | 229 | - Righelli D\*, Koberstein J, Gomes B, Zhang N, Angelini C, Peixoto L, 230 | Risso D. _Differential Enriched Scan 2 ([DEScan2][]): a fast 231 | pipeline for broad peak analysis_. We present DEScan2 a novel 232 | bioconductor package for the analysis of Sono-Seq/Atac-Seq data, 233 | with the aim to facilitate the investigation of broad peak regions 234 | data. 235 | 236 | The method consists of three main steps: 1) a peak caller, 2) a peak 237 | filtering and 3) a method to efficiently compute a count matrix of 238 | the filtered peaks. 239 | 240 | The peak caller in step 1) is a standard moving window scan that 241 | compares the counts within a sliding window to the counts in a 242 | larger region outside the window, using a simple Poisson likelihood, 243 | providing a final z-score for each peak. However, the package can 244 | work with any external peak caller returning results in terms of bed 245 | files, indeed the package provides additional functionalities to 246 | load bed files of peaks and handle them as [GenomicRanges][] 247 | structures. 248 | 249 | The filtering step 2 is aimed to determine if a peak is a “true 250 | peak” on the basis of its replicability in other samples. Basing on 251 | this idea, we developed the filtering step to filter out those peaks 252 | not present in at least a user given number of samples. A further 253 | threshold can be used over the peak score. 254 | 255 | Finally, the third step produces a count matrix where each column is 256 | a sample and each row a filtered peak computed in the filtering 257 | step. The value of the matrix cell is the number of reads for the 258 | peak in the sample. 259 | 260 | Furthermore, our package provides several functionalities for 261 | [GenomicRanges][] data structure handling. One over the others gives 262 | the possibility to split a [GenomicRanges][] over the chromosomes to 263 | speed-up the computations parallelizing them over the chromosomes. 264 | 265 | - Love MI\*, Hickey P, Soneson, C, and Patro R. _Automatic metadata 266 | propagation for RNA-seq_. tximeta performs numerous annotation and 267 | metadata gathering tasks on behalf of users during the import of 268 | transcript quantifications from Salmon into _R / Bioconductor_. The 269 | key idea within tximeta is to store a signature of the transcriptome 270 | sequence, computed and stored by the index and quant functions of 271 | Salmon. This signature acts as the identifying information for later 272 | building out rich annotations and metadata in the background, on 273 | behalf of the user. This should greatly facilitate genomic 274 | workflows, where the user can immediately begin overlapping their 275 | transcriptomic data with other genomic datasets, e.g. epigenetic 276 | tracks such as ChIP or methylation, as the data has been embedded 277 | within an organism and genome context, including the proper genome 278 | version. We seek to reduce wasted time of bioinformatic analysts, 279 | prevent costly bioinformatic mistakes, and promote computational 280 | reproducibility by avoiding situations of annotation and metadata 281 | ambiguity, when files are shared publicly or among collaborators but 282 | critical details go missing. 283 | 284 | - Adithya M, Bhargava A, Wright E\*. _Improving the accuracy of 285 | taxonomic classification for identifying taxa in microbiome 286 | samples_. It has become increasingly clear that the microbiome is an 287 | essential component of human and ecosystem health. Microbiome 288 | studies frequently involve sequencing a taxonomic marker, such as 289 | the 16S rRNA or ITS, to identify the microorganisms that are present 290 | in a sample of interest. Here I will describe a new method, named 291 | IDTAXA, for taxonomic classification of marker gene sequences that 292 | exhibits a substantially lower error rate than previous 293 | approaches. In particular, IDTAXA avoids misclassifying sequences 294 | belonging to novel taxonomic groups that are not represented in 295 | existing taxonomic databases, which is the predominant type of error 296 | made by current classifiers. For example, the popular RDP Classifier 297 | incorrectly assigns 26.0% of novel 16S rRNA sequences to an existing 298 | taxonomic group when the organism actually belongs to a novel 299 | taxonomic group. In contrast, IDTAXA only incorrectly classifies 300 | 13.6% of such sequences, while correspondingly improving on the 301 | fraction of sequences correctly classified to known taxonomic 302 | groups. This has a major impact on the interpretation of microbiome 303 | data because many microbial communities contain a large fraction of 304 | previously undescribed microorganisms that are not yet represented 305 | in taxonomic databases. Furthermore, we find that many taxonomic 306 | databases contain a considerable number of misclassified sequences 307 | that can corrupt the classification process. IDTAXA is able to 308 | automatically identify errors in the training taxonomy so that users 309 | are able to take corrective action. This enables us to 310 | systematically contrast existing taxonomic databases and make 311 | recommendations for their use. Collectively, these improvements 312 | often lead to substantially different classifications on real 313 | microbiome data, which may considerably alter its 314 | interpretation. IDTAXA is available as part of the [DECIPHER][] 315 | package in R (http://DECIPHER.codes). 316 | 317 | - Innes BT\* and Bader GD. _scClustViz - Single-cell RNAseq Cluster 318 | Assessment and Interactive Visualisation_. Single-cell RNA 319 | sequencing is becoming an increasingly popular technology, used both 320 | in large multi-centre projects, and for more directed biological 321 | experiments. A common purpose for applying this technology is the 322 | in silico classification of cell types in a tissue. This is 323 | generally done using one of a myriad of clustering algorithms, based 324 | on the assumption that cells within a cell type are share similar 325 | transcriptomes, which are distinct from other cell types in the 326 | tissue. However, nearly all clustering algorithms have tunable 327 | parameters which affect, either directly or indirectly, the number 328 | of clusters they will return from the data. 329 | 330 | The R Shiny software tool outlined here provides a simple 331 | interactive interface for assessing the biological relevance of 332 | clustering results. Given that cell types are expected to have 333 | distinct gene expression patterns, it uses differential gene 334 | expression between clusters as a metric for assessing overfitting of 335 | clustering (Yuzwa et al., Cell 336 | Reports 2017. DOI:10.1016/j.celrep.2017.12.017). Along with this, 337 | it also provides interactive visualisation of: cluster-specific 338 | distributions of technical factors and other metadata; cluster-wise 339 | gene expression statistics to simplify annotation of cell types and 340 | identification of marker genes; and gene expression distributions 341 | over all cells. 342 | 343 | Interactive user interfaces for single-cell RNAseq analysis already 344 | exist, but this tool fills a distinct niche, as it is explicitly 345 | designed to assist in the biological interpretation of clustering 346 | solutions. Since it is meant to be included in analysis workflows, 347 | it has intentionally been built to be easily customized by the 348 | bioinformatician, as well as used by the non-technical biologist. 349 | 350 | This tool provides an interactive interface for visualisation, 351 | assessment, and biological interpretation of cell-type 352 | classifications in single-cell RNAseq experiments that can be easily 353 | added to existing analysis pipelines, allowing non-technical 354 | biologists easier access to their data. 355 | 356 | [DECIPHER]: https://bioconductor.org/packages/DECIPHER 357 | [DEScan2]: https://bioconductor.org/packages/DEScan2 358 | [DEsingle]: https://bioconductor.org/packages/DEsingle 359 | [GSEABenchmarkeR]: https://bioconductor.org/packages/GSEABenchmarkeR 360 | [GenomicRanges]: https://bioconductor.org/packages/GenomicRanges 361 | [dplyr]: https://bioconductor.org/packages/dplyr 362 | [gwasurvivr]: https://bioconductor.org/packages/gwasurvivr 363 | [plyranges]: https://bioconductor.org/packages/plyranges 364 | -------------------------------------------------------------------------------- /docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 12 | 13 | 14 | 15 | 16 | 18 | 21 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 35 | 36 | 38 | 41 | 42 | 44 | 47 | 48 | 51 | 54 | 56 | 58 | 59 | 60 | 61 | 64 | 67 | 68 | 70 | 71 | 72 | 73 | 74 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 85 | 86 | 88 | 89 | 91 | 92 | 93 | 94 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 107 | 109 | 110 | 112 | 114 | 115 | 117 | 118 | 119 | 120 | 121 | 122 | 124 | 125 | 127 | 129 | 131 | 132 | 134 | 135 | 136 | 137 | 139 | 140 | 141 | 142 | 144 | 145 | 147 | 149 | 150 | 151 | 153 | 154 | 156 | 157 | 158 | 161 | 163 | 166 | 168 | 169 | 170 | 171 | 174 | 175 | 177 | 178 | 179 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 189 | 190 | 192 | 194 | 197 | 199 | 200 | 201 | 203 | 205 | 207 | 209 | 210 | 212 | 213 | 214 | 215 | 217 | 218 | 219 | 220 | 222 | 223 | 225 | 227 | 229 | 231 | 234 | 237 | 238 | 240 | 242 | 244 | 246 | 248 | 249 | 250 | 253 | 255 | 257 | 259 | 262 | 265 | 268 | 271 | 273 | 275 | 277 | 279 | 282 | 283 | 284 | 285 | 287 | 289 | 291 | 293 | 295 | 297 | 300 | 303 | 305 | 307 | 309 | 311 | 313 | 315 | 317 | 319 | 321 | 322 | 323 | 324 | 325 | 326 | 328 | 330 | 331 | 332 | 333 | 334 | 335 | 336 | 337 | --------------------------------------------------------------------------------