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/docs/workshops_full.md:
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1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | ## Workshops
8 |
9 | Join the _Bioconductor_ [#bioc2020](https://community-bioc.slack.com/archives/CLAEUFVAA) and [#bioc2019-workshops](https://community-bioc.slack.com/archives/CJDMYKG2U) channels for up-to-date information
10 |
11 | | 100 Level Workshops |
12 | |---------------------|
13 | | [Introduction to Bioconductor Annotation Resources](https://jmacdon.github.io/Bioc2020Anno/) |  | [GitHub](https://github.com/jmacdon/Bioc2020Anno) | [Docker](https://hub.docker.com/repository/docker/jmacdon/Bioc2020Anno) |
14 | | [A Tidy Transcriptomics introduction to RNA-Seq analyses](https://stemangiola.github.io/bioc_2020_tidytranscriptomics/) |  | [GitHub](https://github.com/stemangiola/bioc_2020_tidytranscriptomics) | [Docker](https://hub.docker.com/repository/docker/stemangiola/bioc_2020_tidytranscriptomics) |
15 | | [Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment](https://waldronlab.github.io/MultiAssayWorkshop/) |  | [GitHub](https://github.com/waldronlab/MultiAssayWorkshop) | [Docker](https://hub.docker.com/repository/docker/waldronlab/MultiAssayWorkshop) |
16 | | [Public data resources and Bioconductor](https://waldronlab.github.io/PublicDataResources/) |  | [GitHub](https://github.com/waldronlab/PublicDataResources) | [Docker](https://hub.docker.com/repository/docker/waldronlab/PublicDataResources) |
17 | | [Annotation of inter-sample epigenetic variation with COCOA](https://databio.github.io/cocoa_workshop_bioc2020/) |  | [GitHub](https://github.com/databio/cocoa_workshop_bioc2020) | [Docker](https://hub.docker.com/repository/docker/databio/cocoa_workshop_bioc2020) |
18 | | [Human RNA-seq data from recount2 and related packages](https://LieberInstitute.github.io/recountWorkshop2020/) |  | [GitHub](https://github.com/LieberInstitute/recountWorkshop2020/) | [Docker](https://hub.docker.com/repository/docker/LieberInstitute/recountWorkshop2020) |
19 |
20 | | 200 Level Workshops |
21 | |---------------------|
22 | | [Best practices for ATAC-seq QC and data analysis](https://haibol2016.github.io/ATACseqQCWorkshop/) |  | [GitHub](https://github.com/haibol2016/ATACseqQCWorkshop) | [Docker](https://hub.docker.com/repository/docker/haibol2016/ATACseqQCWorkshop) |
23 | | [iSEE: Interactive visualization of SummarizedExperiment objects](https://iSEE.github.io/iSEEWorkshop2020/) |  | [GitHub](https://github.com/iSEE/iSEEWorkshop2020) | [Docker](https://hub.docker.com/repository/docker/iSEE/iSEEWorkshop2020) |
24 | | [Functional enrichment analysis of high-throughput omics data](https://waldronlab.github.io/waldronlab/) |  | [GitHub](https://github.com/waldronlab/enrichOmics) | [Docker](https://hub.docker.com/repository/docker/waldronlab/enrichOmics) |
25 | | [Copy number variation analysis with Bioconductor](https://waldronlab.github.io/CNVWorkshop/) |  | [GitHub](https://github.com/waldronlab/CNVWorkshop) | [Docker](https://hub.docker.com/repository/docker/waldronlab/CNVWorkshop) |
26 | | [Comprehensive RNAseq Analysis with oneStopRNAseq](https://radio1988.github.io/oneStopRNAseqWorkshop/) |  | [GitHub](https://github.com/radio1988/oneStopRNAseqWorkshop) | [Docker](https://hub.docker.com/repository/docker/radio1988/oneStopRNAseqWorkshop) |
27 | | [Integrated ChIP-seq Data Analysis Workshop](https://hukai916.github.io/IntegratedChIPseqWorkshop/) |  | [GitHub](https://github.com/hukai916/IntegratedChIPseqWorkshop) | [Docker](https://hub.docker.com/repository/docker/hukai916/IntegratedChIPseqWorkshop) |
28 | | [Hitchhikers Guide to PCA; Demystifying dimensionality reduction in R/Bioconductor](https://aedin.github.io/Frontiers_Supplement/) |  | [GitHub](https://github.com/aedin/Frontiers_Supplement) | [Docker](https://hub.docker.com/repository/docker/aedin/Frontiers_Supplement) |
29 | | [Epidemiology for Bioinformaticians](https://cmirzayi.github.io/epiforbioworkshop/) |  | [GitHub](https://github.com/cmirzayi/epiforbioworkshop) | [Docker](https://hub.docker.com/repository/docker/cmirzayi/epiforbioworkshop) |
30 | | [Biomarker discovery from high throughput screening datasets](https://bhklab.github.io/bioc2020workshop/) |  | [GitHub](https://github.com/bhklab/bioc2020workshop) | [Docker](https://hub.docker.com/repository/docker/bhklab/bioc2020workshop) |
31 |
32 |
33 | | 500 Level Workshops |
34 | |---------------------|
35 | | [Create A Package](https://Kayla-Morrell.github.io/CreateAPackage/) |  | [GitHub](https://github.com/Kayla-Morrell/CreateAPackage) | [Docker](https://hub.docker.com/repository/docker/Kayla-Morrell/CreateAPackage) |
36 | | [Connecting Bioconductor to other bioinformatics tools using Rcwl](https://Liubuntu.github.io/Bioc2020RCWL/) |  | [GitHub](https://github.com/Liubuntu/Bioc2020RCWL) | [Docker](https://hub.docker.com/repository/docker/Liubuntu/Bioc2020RCWL) |
37 | | [Effectively using the DelayedArray framework as a user to support the analysis of large datasets](https://PeteHaitch.github.io/BioC2020_DelayedArray_workshop/) |  | [GitHub](https://github.com/PeteHaitch/BioC2020_DelayedArray_workshop) | [Docker](https://hub.docker.com/repository/docker/PeteHaitch/BioC2020_DelayedArray_workshop) |
38 | | [Introduction to the Terra/AnVIL Cloud-based Genomics Platform](https://waldronlab.github.io/AnVILWorkshop/) |  | [GitHub](https://github.com/waldronlab/AnVILWorkshop) | [Docker](https://hub.docker.com/repository/docker/waldronlab/AnVILWorkshop) |
39 | | [multiHiCcompare: Differential Hi-C Data Analysis Workshop](https://mdozmorov.github.io/HiCcompareWorkshop/) |  | [GitHub](https://github.com/mdozmorov/HiCcompareWorkshop) | [Docker](https://hub.docker.com/repository/docker/mdozmorov/HiCcompareWorkshop) |
40 | | [Trajectory inference across conditions: differential expression and differential progression](https://kstreet13.github.io/bioc2020trajectories/) |  | [GitHub](https://github.com/kstreet13/bioc2020trajectories) | [Docker](https://hub.docker.com/repository/docker/kstreet13/bioc2020trajectories) |
41 | | [Efficient, Scalable, and Reproducible Enrichment Workflows](https://montilab.github.io/hypeR-workshop/) |  | [GitHub](https://github.com/montilab/hypeR-workshop) | [Docker](https://hub.docker.com/repository/docker/montilab/hypeR-workshop) |
42 |
43 | Workshop packages were created using the [BuildABiocWorkshop2020](https://github.com/seandavi/BuildABiocWorkshop2020) template
44 |
45 |
46 |
47 |
52 |
53 |
54 |
55 |
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/docs/index.md:
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1 | ---
2 | layout: default
3 | speakers:
4 | - name: Corrie Painter
5 | inst: Count Me In and Broad Institute
6 | url: https://www.broadinstitute.org/bios/corrie-painter
7 | blurb: "Corrie Painter is the Associate Director of Count Me In and is a research scientist at the Broad Institute of MIT and Harvard. A trained cancer researcher with a Ph.D. in biochemistry, she completed her postdoctoral work in cancer immunology, focused on melanoma. In 2010, Painter was diagnosed with angiosarcoma. She has combined her cancer advocacy and scientific background to engage with patients in order to build and carry out patient-partnered genomics studies. She is also the co-founder of Angiosarcoma Awareness Inc."
8 | - name: Rafael Irizarry
9 | inst: Harvard University
10 | url: https://rafalab.github.io
11 | blurb: "Rafael Irizarry is Professor and Chair of the Department of Data Sciences at the Dana-Farber Cancer Institute and a Professor of Biostatistics at Harvard School of Public Health, and one of the original founders of the Bioconductor Project. Professor Irizarry’s work has focused on problems related to microarray, next-generation sequencing, and genomic data. Currently, he is interested in leveraging his knowledge in translational work, e.g. developing diagnostic tools and discovering biomarkers. During his career, he has co-authored papers on a variety of topics including musical sound signals, infectious diseases, circadian patterns in health, fetal health monitoring, and estimating the effects of Hurricane María in Puerto Rico."
12 | - name: Caroline Uhler
13 | inst: ETH Zurich, Switzerland
14 | url: https://www.carolineuhler.com
15 | blurb: "Caroline Uhler, formerly Associate Professor at MIT in Cambridge, USA, recently joined the ETH Zurich, Switzerland, as Professor of Machine Learning, Statistics and Genomics. Her research focuses on statistics, machine learning and computational biology. In particular, graphical models, causal inference, algebraic statistics and applications to genomics, for example linking the spatial organization of the DNA with gene regulation."
16 | - name: Kylie Ariel Bemis
17 | inst: Northeastern University
18 | url: https://kuwisdelu.github.io
19 | blurb: "Kylie Bemis is a faculty in the Khoury College of Computer Sciences at Northeastern University where she teaches data science and develops curriculum for the MS in Data Science program. Her research interests include machine learning and large-scale statistical computing for bioinformatics. She is active in outreach to the Native American and LGBTQ communities, an enrolled member of the Zuni tribe, and a writer of fiction and poetry."
20 | - name: Fei Chen
21 | inst: Broad Institute
22 | url: https://www.insitubiology.org
23 | blurb: "Fei Chen is currently a Fellow at the Broad Institute. During the course of his doctoral studies in Biological Engineering at MIT, Fei co-invented expansion microscopy (ExM): A breakthrough technique that allows for super-resolution imaging of biological samples with conventional light microscopes. Chen's lab utilizes ExM as a platform for in situ transcriptomics and epigenomics, while continuing to pioneer novel molecular and microscopy tools to uniquely illuminate biological pathways and function."
24 | - name: Aaron Lun
25 | inst: Genentech
26 | url: https://ltla.github.io/about
27 | blurb: "Aaron Lun is a Scientist at Genentech, and previously was a research associate in John Marioni’s group at the CRUK Cambridge Institute and completed a PhD with Gordon Smyth at the Walter and Eliza Hall Institute for Medical Research in Melbourne. Aaron is a prolific contributor to the Bioconductor project, currently especially in the area of single-cell RNA-seq."
28 | - name: Xiaole Shirley Liu
29 | inst: Harvard University
30 | url: https://liulab-dfci.github.io
31 | blurb: "Shirley Liu is a Professor with the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Harvard School of Public Health. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance."
32 | ---
33 |
34 | {% include header.md %}
35 |
36 |
37 | BioC2020 is proceeding as a [Virtual Conference](https://bioc2020.pathable.co/), July 27-31, 2020. BioC2020 highlights current developments within and beyond
38 | the [Bioconductor](https://www.bioconductor.org) project.
39 |
40 | Registration to [virtual Bioc2020](https://bioc2020.pathable.co/) is now closed. We are at capacity of the virtual platform. If registered participants are unable to attend, please let us know. If you have registered, you should receive an email from pathable.com with your login information to the virtual platform.
41 |
42 | ## Conference highlights
43 |
44 |
45 | * Keynotes and contributed talks with live Q&A sessions
46 | * [Workshop materials](./workshops.md) are available
47 | * Posters and Slides are available on the [Bioconductor F1000 Bioc2020 portal](https://f1000research.com/gateways/bioconductor/bioc2020)
48 | * Live tweets of the conference will be posted on [Twitter](https://twitter.com/hashtag/bioc2020) using [#bioc2020](https://twitter.com/hashtag/bioc2020) hashtag
49 | * Videos of talks will be posted on the [Bioconductor YouTube channel](https://www.youtube.com/user/bioconductor) after the conference ([in progress](https://www.youtube.com/watch?v=8MojYYkuLcM&list=PLdl4u5ZRDMQSENJBo6k_wcA27gtydm-bz))
50 | * Join Bioc conversations on Slack [https://bioc-community.herokuapp.com/](https://bioc-community.herokuapp.com/)
51 | * Follow [@Bioconductor](https://twitter.com/Bioconductor) on Twitter [https://twitter.com/Bioconductor](https://twitter.com/Bioconductor)
52 | * For Bioconductor support, use [https://support.bioconductor.org/](https://support.bioconductor.org/)
53 | * Bioconductor website [https://www.bioconductor.org/](https://www.bioconductor.org/)
54 | * Contact Us: [workshop@bioconductor.org](mailto:workshop@bioconductor.org)
55 | * Technical Support for BioC2020: [virtual@conferencedirect.com](mailto:virtual@conferencedirect.com)
56 |
57 |
63 |
64 | Conference flyer [#1](images/flyers/BioC2020Flyerlandscape_lg.pdf), [#2](images/flyers/BioC2020FlyerPortrait.pdf)
65 |
66 |
69 |
70 |
95 |
96 | ## Confirmed Speakers
97 |
98 | {% for s in page.speakers %}
99 | {% assign imgpath = "images/speakers/" | append: s.name | remove: ' ' | append: '.jpg' %}
100 |
22 |
23 | 
27 |
28 |
31 | Conference Home
32 | Registration
33 | Call for submissions
34 |
35 |
43 | - Schedule
44 | - Poster Titles
45 | - Workshops
46 | - Instructions for presenters
47 |
48 | Resources
49 | - Organizing committee
50 |
51 |
52 |
53 | Sponsor Opportunities
54 |
55 | Code of Conduct
56 | Past conferences
57 |
59 |
60 | 
65 |
67 | Conference Sponsors 68 |
69 | 70 |
75 |
76 |
77 |
82 |
83 |
84 |
89 |
90 |
91 |
96 |
97 |
98 |
103 |
104 |
105 |
110 |
111 |
112 |
117 |
118 |
187 |
188 | Bioconductor: https://bioconductor.org
189 | Bioc2020 sticker
190 | Hosted on GitHub Pages
191 | Theme by orderedlist
192 |
| Aedin Culhane | Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health | **Co-chair**, **Sponsorship**, Program: Competitive component, Program: non-competitive component, Code of Conduct |
15 | | 
| Anthony Federico | | Website, Education/Workshop |
16 | | | Ayush Raman | | Outreach, Education/Workshop, Program: Competitive component, Program: non-competitive component |
17 | | 
| Charlotte Soneson | Friedrich Miescher Institute for Biomedical Research | **Program: non-competitive component**, Website, Education/Workshop, Program: Competitive component |
18 | | | Chiaowen Joyce Hsiao | | Program: Competitive component, Program: non-competitive component |
19 | | | Deepak Tanwar | | Program: Competitive component, Program: non-competitive component |
20 | | | Erica Feick | | **Outreach**, Code of Conduct |
21 | | 
| Frederick Boehm | | Outreach, Website, Education/Workshop, Program: Competitive component, Program: non-competitive component, Code of Conduct |
22 | | | Hector Corrada Bravo | | |
23 | | 
| Helena Crowell | Institute of Molecular Life Sciences, University of Zurich, Switzerland | Website, Program: Competitive component, Program: non-competitive component, Code of Conduct |
24 | | | John Hutchinson | | Outreach |
25 | | | Lauren Hsu | | Education/Workshop, Program: Competitive component, Program: non-competitive component, Code of Conduct |
26 | | 
| Laurent Gatto | | |
27 | | 
| Levi Waldron | CUNY Graduate School of Public Health and Health Policy | **Co-chair**, **Code of Conduct**, Education/Workshop, Program: Competitive component, Program: non-competitive component, Sponsorship |
28 | | 
| Lorena Pantano | eGenesis, MA | **Website**, Education/Workshop, Program: non-competitive component, Code of Conduct |
29 | | 
| Lori Shepherd | Roswell Park Comprehensive Cancer Center | Website, Education/Workshop, Program: Competitive component, Program: non-competitive component |
30 | | | Marcel Ramos | | Education/Workshop |
31 | | 
| Martin Morgan | Roswell Park Comprehensive Cancer Center | Website, Program: non-competitive component, Sponsorship, Businness administration, Bioconductor organization |
32 | | 
| Matthew McCall | | **Program: Competitive component** |
33 | | 
| Mikhail Dozmorov | Virginia Commonwealth University | Website, Education/Workshop, Program: Competitive component, Program: non-competitive component |
34 | | | Nathan Sheffield | | Education/Workshop |
35 | | 
| Oriol Senan | | Website, Education/Workshop |
36 | | 
| Peter Hickey | | Code of Conduct |
37 | | 
| Qian Liu | Roswell Park Comprehensive Cancer Center | Website, Program: Competitive component, Program: non-competitive component, Sponsorship |
38 | | | Rafael Irizarry | | Program: non-competitive component, Sponsorship |
39 | | | Ricardo de Matos Simoes | | Education/Workshop, Program: Competitive component, Program: non-competitive component |
40 | | 
| Sean Davis | National Cancer Institute, National Institutes of Health | **Education/Workshop** |
41 | | 
| Simina Boca | Georgetown University | Outreach, Website, Education/Workshop, Program: Competitive component, Program: non-competitive component |
42 | | | Simone Bell | | **Program: non-competitive component**, Sponsorship |
43 | | 
| Tom Carroll | | |
44 | | 
| Venu Thatikonda | German Cancer Research Center, Heidelberg | Outreach, Website |
45 | | 
| Vincent Carey | | |
46 | | 
| Zhezhen Wang | | Outreach, Website, Education/Workshop |
47 |
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/docs/code_of_conduct.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | # Code of Conduct
8 |
9 | This code of conduct is developed for the virtual Bioc2020 conference.
10 |
11 |
12 | ## Social media policy
13 |
14 | 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.
15 |
16 | ## The _Bioconductor_ conference aims to provide a supportive, collegial, and harassment-free environment
17 |
18 | _Bioconductor_ is dedicated to providing a supportive, collegial, and harassment-free
19 | conference experience for everyone, regardless of:
20 | * gender, gender identity and expression, sexual orientation, disability,
21 | physical appearance, body size, race, age, or religion.
22 | * intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
23 |
24 | The Virtual Event Code of Conduct applies to Bioc2020 virtual events and communications, including but not limited to the virtual platform, talks, workshops, poster sessions, social activities, slack, online and social media communications. We do not tolerate harassment, intimidation, or bullying of conference participants. Sexual language and imagery are not appropriate in presentations, communications, in online venues, including chats.
25 |
26 | Conference participants violating these rules may be sanctioned or expelled from the conference with no refund,
27 | at the discretion of the conference organizers. Our anti-harassment policy can be found at [https://bioc2020.bioconductor.org/code_of_conduct](https://bioc2020.bioconductor.org/code_of_conduct)
28 |
29 | ## Examples of unacceptable harassment, intimidation, and bullying behavior
30 |
31 | Harassment includes, but is not limited to:
32 |
33 | * Making comments in chats, to an audience or personally, that belittle or demean another person
34 | * Sharing sexual images online
35 | * Harassing photography or recording
36 | * Sustained disruption of talks or other events
37 | * Unwelcome sexual attention
38 | * Advocating for, or encouraging, any of the above behavior
39 |
40 | Intimidation and bullying include, but are not limited to:
41 |
42 | * Aggressive or browbeating behavior directed at someone during a public presentation
43 | * Mocking or insulting another person's intellect, work, perspective, or question/comment
44 | * Making reference to someone's gender, gender identity and expression, sexual orientation, disability,
45 | physical appearance, body size, race, age, religion, or other personal attributes in the context of a scientific
46 | discussion
47 | * Deliberately making someone feel unwelcome
48 |
49 | ### Enforcement
50 |
51 | Participants asked to stop any harassing behavior are expected to comply immediately.
52 |
53 | If a participant engages in harassing behavior, event organizers 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.
54 |
55 | Event organizers 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.
56 |
57 | We expect participants to follow these rules at all event venues and event-related online activities.
58 |
59 | ### Reporting
60 |
61 | If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible.
62 | Harassment and other code of conduct violations reduce the value of our event for everyone.
63 | We want you to be happy at our event. People like you make our event a better place.
64 |
65 | You can make a report either personally or anonymously.
66 |
67 | #### Anonymous or Non-anonymous Report
68 |
69 | You can make an anonymous or non-anonymous report here: [https://tinyurl.com/bioccomplaint](https://tinyurl.com/bioccomplaint). It is a free-form text box that will be forwarded to conference organizers.
70 |
71 | 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.
72 |
73 | #### Personal Report
74 |
75 | You can make a personal report with any of the conference anti-harassment committee: Aedin Culhane, Levi Waldron, and Laurent Gatto.
76 |
77 | 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.
78 |
79 | 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.
80 |
81 | ### Code of Conduct violation reports
82 |
83 | * Email: [code-of-conduct@bioconductor.org](mailto:workshop@bioconductor.org?subject=BioC2019%20code-of-conduct)
84 | * Anonymous Code of Conduct violation reports: [https://tinyurl.com/bioccomplaint](https://tinyurl.com/bioccomplaint)
85 | * Law enforcement emergency number: 911
86 |
87 | ### Code of Conduct Committee
88 |
89 | | Photo | Name |
90 | |-------|------|
91 | | | [Aedin Culhane](mailto:aedin@jimmy.harvard.edu?subject=BioC2019%20code-of-conduct) |
92 | | | [Levi Waldron](mailto:lwaldron.research@gmail.com?subject=BioC2019%20Code-of-conduct) |
93 | | | [Laurent Gatto](mailto:laurent.gatto@uclouvain.be?subject=BioC2019%20Code-of-conduct) |
94 |
95 |
96 |
183 |
--------------------------------------------------------------------------------
/docs/schedule.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | # Agenda
8 |
9 | All time is US Eastern Time. All sessions include Q&A time.
10 |
11 |
12 | | Time | Track | Name |
13 | |------------------------|----------|--------------------------------------------------------------------------------------------------------------------------------|
14 | | **Monday, 7/27/2020** | |
15 |
16 |
17 |
18 |
19 | |
20 | | 8:00 AM | Community | Open breakfast meeting |
21 | | 8:30 AM | Talk | [Talk, Martin Morgan, Introduction & Welcome](https://youtu.be/LJT9HjKiipU) |
22 | | 9:00 AM | Talk | [Keynote, Rafael Irizarry. Probabilistic Gene Expression Signatures for Single Cell RNA-seq Data](https://youtu.be/8MojYYkuLcM) |
23 | | 10:00 AM | Talk | [Contributed Talk 1, Yi Wang, Ting Huang, Simina Boca, Phillipe Boilleau](https://youtu.be/uCf24yYstKU) |
24 | | 11:00 AM | Workshop | [100: Levi Waldron, Public data resources in Bioconductor](https://youtu.be/wxY1I08Fz2o) |
25 | | 12:00 PM | Community | [Birds of a Feather: On Standards for Accessible and Interpretable Visualizations](https://youtu.be/gGkAvO4zGC8) |
26 | | 12:00 PM | Community | Talk with the BioC Core Team |
27 | | 1:00 PM | Workshop | [100: Chloe Mirzayi, A workshop for concepts of epidemiology](https://youtu.be/gRX7ybM6SmA) |
28 | | 2:00 PM | Workshop | [100: John Lawson, Annotating inter-sample DNA methylation and ATAC-seq variation with COCOA](https://youtu.be/raMA0IVWVUQ) |
29 | | 3:00 PM | Workshop | [100: Leonardo Collado-Torres, Human RNA-seq data from recount2 and related packages](https://youtu.be/EDe0e_VaENQ) |
30 | | 4:00 PM | Workshop | [100: James W. MacDonald, Introduction to Bioconductor annotation resources](https://youtu.be/QKGwf8pKb6A) |
31 | | 5:00 PM | Workshop | [100: Stefano Mangiola, A tidy transcriptomics introduction to RNA-Seq analyses](https://youtu.be/5Cgnpwv19Jk) |
32 | | **Tuesday, 7/28/2020** | |
33 | |
34 | | 8:00 AM | Community | Open breakfast meeting |
35 | | 9:00 AM | Workshop | [200: Ludwig Geistlinger, Functional enrichment analysis of high-throughput omics data](https://youtu.be/n0vVwuQSZkg) |
36 | | 10:00 AM | Workshop | [200: Haibo Liu, Best practices for ATAC-seq QC and data analysis](https://youtu.be/VZFUu_cJxyI) |
37 | | 11:00 AM | Workshop | [200: Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Copy number variation analysis with Bioconductor](https://youtu.be/MZL1HtMjyL4) |
38 | | 12:00 PM | Community | Birds of a Feather Talks |
39 | | 12:00 PM | Community | [Talk with the BioC Technical Advisory Board](https://youtu.be/QIByL02DSzI) |
40 | | 1:00 PM | Workshop | [200: Charlotte Soneson, Aaron Lun, Interactive visualization of SummarizedExperiment objects with iSEE](https://youtu.be/qmoJtL8b438) |
41 | | 2:00 PM | Talk | [Keynote, Kylie Bemis, Out-of-memory computing with matter](https://youtu.be/AQkAlkuhj70) |
42 | | 3:00 PM | Talk | [Contributed Talks 2, Daniel Bunis, Koen Van den Berge, F. William Townes. Lauren Hsu](https://youtu.be/TyHoVhDk9NU) |
43 | | 4:00 PM | Workshop | [200: Lihua Julie Zhu, Jianhong Ou, CRISPRseek for design target-specific gRNAs for the CRISPR genome editing system including base editor and prime editor](https://youtu.be/Kj2yzZ_45cU) |
44 | | 5:00 PM | Workshop | [200: Kai Hu, Integrated ChIP-seq data analysis workshop](https://youtu.be/EAxFrz_F4bg) |
45 | | **Wednesday, 7/29/2020** | | |
46 | | 8:00 AM | Community | [Presentation of the BioC Commuity Advisory Board](https://youtu.be/noHn5fEbBwA) |
47 | | 8:40 AM | Community | [Presentation of the BioC Awards Ceremony](https://youtu.be/noHn5fEbBwA) |
48 |
49 | | 9:00 AM | Talk | [Keynote, Corrie Painter, Count Me In, Partnering with patients to accelerate the pace of cancer research](https://youtu.be/Ip8_AHqeBXM) |
50 | | 10:00 AM | Community | [Birds of a Feather: CDSB Community Meeting](https://youtu.be/U-ZFWmSxSOE) |
51 | | 11:00 AM | Workshop | [200: Marcel Ramos, MultiAssayExperiment and curatedTCGAData Bioconductor 2020 workshop](https://youtu.be/Vh0hVVUKKFM) |
52 | | 12:00 PM | Poster | Poster Session A |
53 | | 1:00 PM | Workshop | [200: Aedin Culhane, Lauren Hsu, A introduction to matrix factorization, svd and principal component analysis](https://youtu.be/sP6rry9Yf2w) |
54 | | 2:00 PM | Talk | [Keynote, Fei Chen, Slide-seq: a platform for understanding cellular circuits in tissue](https://youtu.be/UwoSLWlyC74) |
55 | | 3:00 PM | Talk | [Contributed Talks 3, Lukas M. Weber, Dario Righelli, Lambda Lu, Ellis Patrick](https://youtu.be/bD_zaBpzCKY) |
56 | | 4:00 PM | Workshop | [200: Petr Smirnov, Arvind Mer, Christopher Eeles, A workshop on discovering biomarkers from high through put response screens](https://youtu.be/i2_b6JeN6Vc) |
57 | | 5:00 PM | Workshop | [500: Qian Liu, Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines in CWL](https://youtu.be/JCxoQwz-95s) |
58 | | **Thursday, 7/30/3030** | | |
59 | | 8:00 AM | Workshop | [500: Peter F. Hickey, Effectively Using the DelayedArray Framework to Support the Analysis of Large Datasets](https://youtu.be/0x7Q4oyM7uA) |
60 | | 9:00 AM | Workshop | [100: Sehyun Oh, Levi Waldron, Cloud-based genomics using Terra/AnVIL](https://youtu.be/KYBDeDIf5tQ) |
61 | | 10:00 AM | Workshop | [500: Mikhail Dozmorov, Detection of differentially interacting chromatin regions from multiple Hi-C datasets](https://youtu.be/f4RaQVwPMzo) |
62 | | 11:00 AM | Workshop | [500: Kayla Interdonato, Material on how to create and submit a package to Bioconductor](https://youtu.be/fq3kx6FZ6lY) |
63 | | 12:00 PM | Community | Birds of a Feather: Ten simple rules for thriving in bioinformatics research |
64 | | 12:00 PM | Community | [Talk with the BioC Core Team](https://youtu.be/a0EB893-O_A) |
65 | | 1:00 PM | Talk | [Lightning Talks, Session #2](https://youtu.be/DOYepK47RH8) |
66 | | 2:00 PM | Talk | [Keynote, X Shirley Liu, Computational modeling of protein degradation in tumors](https://youtu.be/WhNFqi5eP3I) |
67 | | 3:00 PM | Talk | [Contributed Talks 4, Anthony Mammoliti, Shradda Pai, Gabriel Odom. Ruth Schmidt](https://youtu.be/GdHB9jwios8) |
68 | | 4:00 PM | Workshop | 500: Anthony Federico, Efficient, scalable, and reproducible enrichment workflows |
69 | | 4:00 PM | Community | [Birds of a Feather: On Standards for Accessible and Interpretable Visualizations - Follow Up](https://youtu.be/M18OL-t1AKs) |
70 | | 5:00 PM | Workshop | [200: Michael Love, Importing alevin scRNA-seq counts into R/Bioconductor](https://youtu.be/FL5GFXeBuvc) |
71 | | **Friday, 7/31/2020** | | |
72 | | 8:00 AM | Poster | Poster Session B |
73 | | 9:00 AM | Talk | [Keynote, Caroline Uhler, Multi-Domain Data Integration: From Observations to Mechanistic Insights](https://youtu.be/EyUrToDdMWY) |
74 | | 10:00 AM | Talk | [Contributed Talks 5, Emma Jablonski, Shian Su, Hena Ramay, Jayaram Kancheria](https://youtu.be/MToJ_oOXm_c) |
75 | | 11:00 AM | Workshop | [500: Kelly Street, Koen Van den Berge, Trajectory inference across conditions: differential expression and differential progression](https://youtu.be/Fbd08bIv4yk) |
76 | | 12:00 PM | Community | Birds of a Feather: Reproducible environments for integrated computational workflows |
77 | | 12:00 PM | Community | [Talk with the BioC Core Team](https://youtu.be/hf2qzpK81II) |
78 | | 1:00 PM | Talk | [Lightning Talks](https://youtu.be/ameCkKFvm0I) |
79 | | 2:00 PM | Talk | [Keynote, Aaron Lun, Making the infrastructure sausage: tales of Bioconductor package development](https://youtu.be/wQJbSh-NHeg) |
80 | | 3:00 PM | Talk | [Contributed Talks 6, Charlotte Soneson, Davide Risso, Anthony Sonrel, Stephanie Hicks](https://youtu.be/09DxXqZ2KJo) |
81 | | 4:00 PM | Talk | Closing Remarks |
82 | | 4:30 PM | | Happy Hour |
83 |
84 |
85 |
86 |
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/docs/workshops.md:
--------------------------------------------------------------------------------
1 | ---
2 | layout: default
3 | ---
4 |
5 | {% include header.md %}
6 |
7 | ## Workshops
8 |
9 | Join the *Bioconductor*
10 | [\#bioc2020](https://community-bioc.slack.com/archives/CLAEUFVAA) and
11 | [\#bioc2020-workshops](https://community-bioc.slack.com/archives/C015QR5FCGN)
12 | channels for up-to-date information.
13 |
14 | ### 100 Level Workshops
15 |
16 | | Workshop | Source | Docker |
17 | | :----------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------- |
18 | | [Introduction to Bioconductor annotation resources](https://jmacdon.github.io/Bioc2020Anno/) | [](https://github.com/jmacdon/Bioc2020Anno) | [](https://hub.docker.com/repository/docker/jmacdon/bioc2020anno) |
19 | | [A Tidy Transcriptomics introduction to RNA-Seq analyses](https://stemangiola.github.io/bioc_2020_tidytranscriptomics/) | [](https://github.com/stemangiola/bioc_2020_tidytranscriptomics) | [](https://hub.docker.com/repository/docker/stemangiola/bioc_2020_tidytranscriptomics) |
20 | | [Public Data Resources in Bioconductor](https://waldronlab.io/PublicDataResources/) | [](https://github.com/waldronlab/PublicDataResources) | [](https://hub.docker.com/repository/docker/waldronlab/publicdataresources) |
21 | | [Annotating inter-sample DNA methylation and ATAC-seq variation with COCOA](http://databio.org/cocoa_workshop_bioc2020/) | [](https://github.com/databio/cocoa_workshop_bioc2020) | [](https://hub.docker.com/repository/docker/databio/cocoa_workshop_bioc2020) |
22 | | [Human RNA-seq data from recount2 and related packages](https://LieberInstitute.github.io/recountWorkshop2020/) | [](https://github.com/LieberInstitute/recountWorkshop2020) | [](https://hub.docker.com/repository/docker/lcollado/recountworkshop2020) |
23 | | [Cloud-based Genomics using Terra/AnVIL](https://waldronlab.github.io/AnVILWorkshop/) | [](https://github.com/waldronlab/AnVILWorkshop) | [](https://hub.docker.com/repository/docker/shbrief/anvilworkshop) |
24 | | [Epidemiology for Bioinformaticians Workshop](https://cmirzayi.github.io/EpiForBioWorkshop2020/) | [](https://github.com/cmirzayi/EpiForBioWorkshop2020) | [](https://hub.docker.com/repository/docker/cmirzayi/epiforbioworkshop2020) |
25 |
26 |
27 |
28 | ### 200 Level Workshops
29 |
30 | | Workshop | Source | Docker |
31 | | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :--------------------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------------------------------------------- |
32 | | [Best practices for ATAC-seq QC and data analysis](https://haibol2016.github.io/ATACseqQCWorkshop/) | [](https://github.com/haibol2016/ATACseqQCWorkshop) | [](https://hub.docker.com/repository/docker/nemat1976/atacseqqcworkshop_2020) |
33 | | [Interactive Visualization of SummarizedExperiment Objects with iSEE](https://iSEE.github.io/iSEEWorkshop2020) | [](https://github.com/iSEE/iSEEWorkshop2020) | [](https://hub.docker.com/repository/docker/iseedevelopers/iseeworkshop2020) |
34 | | [Functional enrichment analysis of high-throughput omics data](https://waldronlab.github.io/enrichOmics/) | [](https://github.com/waldronlab/enrichOmics) | [](https://hub.docker.com/repository/docker/ludwigg/enrichomics) |
35 | | [Copy number variation analysis with Bioconductor](https://waldronlab.github.io/CNVWorkshop) | [](https://github.com/waldronlab/CNVWorkshop) | [](https://hub.docker.com/repository/docker/ludwigg/cnvworkshop) |
36 | | [MultiAssayExperiment and curatedTCGAData Bioconductor 2020 Workshop](https://waldronlab.github.io/MultiAssayWorkshop/) | [](https://github.com/waldronlab/MultiAssayWorkshop) | [](https://hub.docker.com/repository/docker/mr148/multiassayworkshop) |
37 | | [CRISPRseek and GUIDEseq for designing target-specific gRNAs for the CRISPR genome editing system; Motif analysis with motifStack and dagLogo](https://LihuaJulieZhu.github.io/CRISPRseekGUIDEseqBioc2020Workshop/) | [](https://github.com/LihuaJulieZhu/CRISPRseekGUIDEseqBioc2020Workshop/) | [](https://hub.docker.com/repository/docker/lihuajuliezhu/crisprseekguideseqbioc2020workshop) |
38 | | [Integrated ChIP-seq analysis workshop](https://hukai916.github.io/IntegratedChIPseqWorkshop/) | [](https://github.com/hukai916/IntegratedChIPseqWorkshop) | [](https://hub.docker.com/repository/docker/hukai916/integratedchipseqanalysis_workshop) |
39 | | [An introduction to matrix factorization and principal component analysis in R](https://aedin.github.io/PCAworkshop/) | [](https://github.com/aedin/PCAworkshop) | [](https://hub.docker.com/repository/docker/aculhane/pcabiocworkshop2020) |
40 | | [A workshop on discovering biomarkers from high through put response screens](https://bhklab.github.io/bioc2020workshop) | [](https://github.com/bhklab/bioc2020workshop) | [](https://hub.docker.com/repository/docker/bhklab/gxbioc2020workshop) |
41 | | [Importing alevin scRNA-seq counts into R/Bioconductor](https://mikelove.github.io/alevin2bioc/) | [](https://github.com/mikelove/alevin2bioc) | [](https://hub.docker.com/repository/docker/mikelove/alevin2bioc) |
42 |
43 |
44 |
45 | ### 500 Level Workshops
46 |
47 | | Workshop | Source | Docker |
48 | | :----------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------- |
49 | | [Material on how to create and submit a package to Bioconductor](https://kayla-morrell.github.io/CreateAPackage/) | [](https://github.com/Kayla-Morrell/CreateAPackage) | [](https://hub.docker.com/repository/docker/kaylainterdonato01/createapackage) |
50 | | [Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines in CWL](https://Liubuntu.github.io/Bioc2020RCWL) | [](https://github.com/Liubuntu/Bioc2020RCWL) | [](https://hub.docker.com/repository/docker/liubuntu/bioc2020rcwl) |
51 | | [Effectively Using the DelayedArray Framework to Support the Analysis of Large Datasets](https://petehaitch.github.io/BioC2020_DelayedArray_workshop/) | [](https://github.com/PeteHaitch/BioC2020_DelayedArray_workshop) | [](https://hub.docker.com/repository/docker/petehaitch/bioc2020_delayedarray_workshop) |
52 | | [Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets](https://mdozmorov.github.io/HiCcompareWorkshop/) | [](https://github.com/mdozmorov/HiCcompareWorkshop) | [](https://hub.docker.com/repository/docker/mdozmorov/hiccompareworkshop) |
53 | | [Trajectory inference across conditions: differential expression and differential progression](https://kstreet13.github.io/bioc2020trajectories) | [](https://github.com/kstreet13/bioc2020trajectories) | [](https://hub.docker.com/repository/docker/kstreet13/bioc2020trajectories) |
54 | | [Efficient, Scalable, and Reproducible Enrichment Workflows](https://montilab.github.io/hypeR-workshop/) | [](https://github.com/montilab/hypeR-workshop) | [](https://hub.docker.com/repository/docker/montilab/hyperworkshop) |
55 |
56 |
57 |
58 | Workshops with preinstalled dependencies can be run locally using
59 | Docker.
60 |
61 | - `docker pull