22 | {{ end }}
23 | {{ end }}
24 | {{ end }}
25 |
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1 | {{ if isset .Site.Params.widgets "search" }}
2 | {{ if .Site.Params.widgets.search }}
3 |
4 |
5 |
6 |
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7 |
8 |
9 |
10 |
19 |
20 |
21 | {{ end }}
22 | {{ end }}
23 |
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/data/abstracts/day1_1315_Workshop_paper25.yaml:
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1 | title: "Introduction to Bioconductor annotation resources*"
2 | paper: "paper25"
3 | session_type: "Workshop"
4 | authors: "James MacDonald"
5 | presenting_author: "James MacDonald"
6 | affiliation: "University of Washington"
7 | abstract: "There are various annotation packages provided by the Bioconductor project that can be used to incorporate additional information to results from high-throughput experiments. This can be as simple as mapping Ensembl IDs to corresponding HUGO gene symbols, to much more complex queries involving multiple data sources. In this workshop we will cover the various classes of annotation packages, what they contain, and how to use them efficiently. "
8 | time: "13:15"
9 | github: "https://github.com/jmacdon/Bioc2022Anno"
10 | twitter: ""
11 | youtube: "https://www.youtube.com/watch?v=rFNBTrTcY78"
12 | day: "day1"
13 | talks: ""
14 | level: "Beginner"
15 | details: "https://jmacdon.github.io/Bioc2022Anno/"
16 | orchestra: "yes"
17 |
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1 | {{ if isset .Site.Params "carousel" }}
2 | {{ if .Site.Params.carousel.enable }}
3 | {{ if gt (len .Site.Data.carousel) 0 }}
4 |
5 |
6 |
7 |
8 |
9 | {{ range sort .Site.Data.carousel "weight" }}
10 |
37 |
38 |
39 |
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/LICENSE:
--------------------------------------------------------------------------------
1 | MIT License
2 |
3 | Copyright (c) 2020 Mikhail Dozmorov
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/LICENSE:
--------------------------------------------------------------------------------
1 | The MIT License (MIT)
2 |
3 | Copyright (c) 2016 DevCows
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/themes/hugo-universal-theme/layouts/partials/see_more.html:
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1 | {{ if isset .Site.Params "see_more" }}
2 | {{ if .Site.Params.see_more.enable }}
3 |
4 |
5 |
July 24, 2024: Call for Talks, Workshops and Conference Access awards open
15 |
August 26, 2024: Call for Talks and Workshops close
16 |
September 30, 2024: Notification of abstract decision
17 |
Nov 7-8, 2024: The BioCAsia 2024 conference
18 |
19 |
20 |
21 | ## Submission types
22 |
23 | ### Talks (Talk submission form)
24 |
25 | Focused on a package, an application note, or a current research presentation. Presentations seeking collaboration or input from the community are encouraged.
26 |
27 |
28 | ### Software demo/Workshop (Workshop submission form)
29 | 60 mins or 120 mins demonstration of a software package or workflow.
30 |
31 |
32 |
33 | ### BioCAsia Conference Access Award (Application form)
34 | The Conference Access Award will cover the registration fees for the BioCAsia 2024 conference.
35 |
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/themes/hugo-universal-theme/layouts/partials/features.html:
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1 | {{ if isset .Site.Params "features" }}
2 | {{ if .Site.Params.features.enable }}
3 | {{ if gt (len .Site.Data.features) 0 }}
4 |
5 |
36 | {{ end }}
37 |
38 | {{ if eq .github "" }}
39 |
{{ .github }}
40 | {{ else }}
41 |
42 | {{ end }}
43 |
44 | {{ if eq .youtube "" }}
45 |
{{ .youtube }}
46 | {{ else }}
47 |
48 | {{ end }}
49 |
50 | {{ end }}
51 | {{ end }}
52 | {{ end }}
53 |
54 |
55 |
56 |
57 | {{- end -}}
58 |
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/data/abstracts/day1_0900_Shorttalk_paper31.yaml:
--------------------------------------------------------------------------------
1 | title: "Predictive Modelling Of Dataset-Specific Single-Cell RNA-Seq Pipeline Performance"
2 | paper: "paper31"
3 | session_type: "Short talk"
4 | authors: "Cindy Fang, Alina Selega, Kieran R. Campbell"
5 | presenting_author: "Cindy Fang"
6 | affiliation: "University of Toronto"
7 | abstract: "The advent of single-cell RNA-sequencing (scRNA-seq) has driven a plethora of computational methods development for all analysis stages, including filtering, normalisation, and clustering. With many choices for each step in the analysis pipeline available to practitioners, selecting the optimal workflow can be a difficult task. Considering an unrealistically simplistic example with only 3 analysis steps (e.g. filtering, normalisation, clustering), 4 methods for each step, and each method having only 2 possible parameter combinations gives $(4\times2)^3 = 512$ possible pipelines. Given the far larger set of possibilities for steps, methods, and parameters, in practice the number of sensible pipelines that could be applied to scRNA-seq data is likely in the high thousands if not millions. While multiple existing benchmark studies can recommend the best performing method on average for each step, these are ultimately dependent on dataset characteristics. This leads to an interesting question: is it possible to predict how well a given pipeline will perform on a certain dataset? To begin to answer this, we have created a dataset consisting of the performance of 288 scRNA-seq clustering pipelines on 86 human datasets, quantifying performance using a variety of cluster purity metrics and gene set enrichment scores. Using this dataset, we build a series of supervised machine learning models that are able to predict pipeline performance for an unseen dataset given pipeline parameters and dataset characteristics. We find that on unseen datasets with author-provided ‘ground truth’ labels, pipelines predicted to perform well have clustering outputs that significantly correlate with these labels compared to those that were not predicted to perform well. Finally, by examining correlations of prediction performance with dataset-specific characteristics such as the number of genes, we identify which biological factors may impact the ability to predict pipeline performance. "
8 | time: "09:00"
9 | github: ""
10 | twitter: ""
11 | youtube: "https://youtu.be/AkElObGncWE"
12 | day: "day1"
13 | talks: ""
14 | details: ""
15 |
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/themes/hugo-universal-theme/layouts/_default/single.html:
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1 |
2 |
3 |
4 | {{ partial "head.html" . }}
5 |
6 |
7 |
8 |
Registration for the BioCAsia 2024 conference is managed through the ABACBS conference
5 |
BioCAsia 2024 will be held in Sydney, Australia
6 |
(Location: Abercrombie Building, The University of Sydney)
7 |
8 |
9 | The 2024 Bioconductor Asia conference aims to bring together researchers and scientists to exchange scientific knowledge and foster collaboration within the bioinformatics community both across the Asia-Pacific region and globally. The conference will also offer a series of hands-on workshops on R and Bioconductor, aimed at advancing education and training in computational biomedical sciences.
10 |
112 |
113 |
114 | {{ partial "scripts.html" . }}
115 |
116 |
117 |
118 |
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/static/workshops-status.Rmd:
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1 | ---
2 | output: github_document
3 | ---
4 |
5 | ## Workshops
6 |
7 | ```{r, eval=FALSE,echo=FALSE}
8 | # run this to create the workshops.md file
9 | rmarkdown::render("workshops-status.Rmd",
10 | rmarkdown::md_document(
11 | variant="gfm", preserve_yaml = FALSE
12 | )
13 | )
14 | writeLines(c(
15 | "---
16 | layout: default
17 | ---
18 |
19 | {% include header.md %}
20 | ",
21 | readLines("workshops-status.md")
22 | ),
23 | con = file("workshops-status.md")
24 | )
25 | ```
26 |
27 | ```{r, include=FALSE}
28 | setClass("Workshop", representation(
29 | title = "character", # Workshop title
30 | github = "character", # GitHub repository 'owner/repo'
31 | docker = "character", # Docker repository 'owner/repo'
32 | badge = "character" # path to the GitHub workflow badge
33 | ))
34 | Workshop <- function(...) {
35 | new("Workshop", ...)
36 | }
37 | setGeneric(
38 | "renderTibbleRow",
39 | function(x) standardGeneric("renderTibbleRow")
40 | )
41 | setMethod("renderTibbleRow", "Workshop", function(x) {
42 | github_user_repo <- strsplit(x@github, "/")[[1]]
43 | github_user <- github_user_repo[1]
44 | github_repo <- github_user_repo[2]
45 | workshop_link <- sprintf("[%s](https://%s.github.io/%s) ", x@title, github_user, github_repo)
46 | source_link <- sprintf("[](https://github.com/%s)", x@github)
47 | docker_image <- htmltools::HTML(sprintf(""))
48 | docker_image_url <- sprintf("https://hub.docker.com/r/%s", x@docker)
49 | docker_link <- sprintf("[%s](%s)", docker_image, docker_image_url)
50 | status_badge <- sprintf("[](https://github.com/%s/actions)", x@github, x@badge, x@github)
51 | tibble::tibble(
52 | Workshop = workshop_link,
53 | Source = source_link,
54 | Docker = docker_link,
55 | Status = status_badge
56 | )
57 | })
58 | ```
59 |
60 | ```{r, include=FALSE}
61 | Paper9 <- Workshop(
62 | title = "Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment",
63 | github = "stemangiola/bioc2021_tidytranscriptomics",
64 | docker = "stemangiola/bioc2021_tidytranscriptomics",
65 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
66 | )
67 | Paper27 <- Workshop(
68 | title = "Dimension Reduction for Beginners",
69 | github = "aedin/PCAworkshop",
70 | docker = "aculhane/pcabiocworkshop2020",
71 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
72 | )
73 | Paper40 <- Workshop(
74 | title = "Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment",
75 | github = "waldronlab/MultiAssayWorkshop",
76 | docker = "mr148/multiassayworkshop",
77 | badge = "MAEWorkshopCheck/badge.svg"
78 | )
79 | Paper50 <- Workshop(
80 | title = "Effectively using the DelayedArray framework to support the analysis of large datasets",
81 | github = "PeteHaitch/BioC2021_DelayedArray_workshop",
82 | docker = "petehaitch/bioc2021_delayedarray_workshop",
83 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
84 | )
85 | Paper68 <- Workshop(
86 | title = "Introduction to Bioconductor annotation resources",
87 | github = "jmacdon/Bioc2021Anno",
88 | docker = "jmacdon/bioc2021anno",
89 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
90 | )
91 | Paper78 <- Workshop(
92 | title = "Reproducing a single-cell proteomics data analysis using QFeatures and scp",
93 | github = "lgatto/QFeaturesScpWorkshop2021",
94 | docker = "lgatto/qfeaturesscpworkshop2021",
95 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
96 | )
97 | Paper80 <- Workshop(
98 | title = "Trajectory inference across conditions: differential expression and differential progression",
99 | github = "HectorRDB/bioc2021trajectories",
100 | docker = "HectorRDB/bioc2021trajectories",
101 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
102 | )
103 | Paper81 <- Workshop(
104 | title = "systemPipe: Workflow and Visualization Toolkit",
105 | github = "systemPipeR/systemPipeWorkshop2021",
106 | docker = "systempipe/systempipeworkshop2021",
107 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
108 | )
109 | Paper112 <- Workshop(
110 | title = "Building Carpentries-based Bioconductor Lessons",
111 | github = "jdrnevich/BuildACarpentriesWorkshop",
112 | docker = "jdrnevich/buildacarpentriesworkshop",
113 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
114 | )
115 | Paper121 <- Workshop(
116 | title = "Epidemiology for Bioinformaticians",
117 | github = "cmirzayi/epiforbioworkshop2021",
118 | docker = "cmirzayi/epiforbioworkshop2021",
119 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
120 | )
121 | Paper124 <- Workshop(
122 | title = "Introduction to the Terra/AnVIL Cloud-based Genomics Platform",
123 | github = "waldronlab/AnVILWorkshop",
124 | docker = "shbrief/anvilworkshop",
125 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
126 | )
127 | ```
128 |
129 | ```{r, echo=FALSE}
130 | workshop_table <- dplyr::bind_rows(
131 | renderTibbleRow(Paper9),
132 | renderTibbleRow(Paper27),
133 | renderTibbleRow(Paper40),
134 | renderTibbleRow(Paper50),
135 | renderTibbleRow(Paper68),
136 | renderTibbleRow(Paper78),
137 | renderTibbleRow(Paper80),
138 | renderTibbleRow(Paper81),
139 | renderTibbleRow(Paper112),
140 | renderTibbleRow(Paper121),
141 | renderTibbleRow(Paper124)
142 | )
143 | knitr::kable(workshop_table,
144 | format = "markdown",
145 | col.names = c("Workshop", "Source ", "Docker ", "Status"),
146 | align=c("l", "c", "c", "l")
147 | )
148 | ```
149 |
150 |
151 |
152 | Find out more details on the [Workshops](/workshops) page!
153 |
154 |
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2 |
134 |
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/themes/hugo-universal-theme/layouts/partials/head.html:
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1 |
2 |
3 |
4 |
5 |
6 | {{ $title_plain := .Title | markdownify | plainify }}
7 | {{ $title_plain }}
8 |
9 | {{ $keywords := .Site.Params.defaultKeywords | default (slice "" | first 0) }}
10 | {{ if isset .Params "tags" }}{{ range .Params.tags }}{{ $keywords = $keywords | append . }}{{ end }}{{ end }}
11 | {{ if isset .Params "keywords" }}{{ range .Params.keywords }}{{ $keywords = $keywords | append . }}{{ end }}{{ end }}
12 | {{ if gt (len $keywords) 0 }}
13 |
14 | {{ end }}
15 | {{ $description_plain := default .Site.Params.defaultDescription .Description | markdownify | plainify }}
16 |
17 |
18 | {{ hugo.Generator }}
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 | {{ with .Site.Params.style }}
32 |
33 | {{ else }}
34 |
35 | {{ end }}
36 |
37 |
38 |
39 |
40 |
41 | {{ `
42 |
46 | ` | safeHTML }}
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 |
60 | {{ $is_blog := and (eq .Type "blog") (eq .Kind "page") }}
61 | {{ $has_image := isset .Params "banner" }}
62 | {{ $image := cond $has_image .Params.banner (.Site.Params.default_sharing_image | default "img/sharing-default.png") }}
63 | {{ $is_valid_image := print "static/" $image | fileExists }}
64 | {{ if $is_valid_image }}
65 | {{ $image_ext := path.Ext $image }}
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
74 | {{ with .Params.banner_alt }}{{ end }}
75 | {{ $image_local := printf "/static/%s" $image}}
76 | {{ with (imageConfig $image_local) }}
77 |
78 |
79 | {{ end }}
80 | {{ end }}
81 | {{ with .Lastmod }}{{ end }}
82 | {{ if $is_blog }}
83 | {{ with .Param "facebook_site" }}{{ end }}
84 | {{ with .Param "facebook_author" }}{{ end }}
85 | {{ with .Params.categories }}{{ end }}
86 | {{ range .Params.tags }}
87 | {{ end }}
88 | {{ if gt .ExpiryDate .PublishDate }}{{ end }}
89 | {{ with .PublishDate }}{{ end }}
90 | {{ with .Lastmod }}{{ end }}
91 | {{ end }}
92 |
93 |
94 |
95 | {{ with .Param "twitter_site" }}{{ end }}
96 |
97 | {{ if $is_valid_image }}
98 |
99 | {{ end }}
100 |
101 | {{ with .Param "twitter_author" }}{{ end }}
102 |
103 |
104 |
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/content/code.md:
--------------------------------------------------------------------------------
1 | +++
2 | title = "Code of conduct"
3 | description = "Code of conduct"
4 | +++
5 |
6 | This code of conduct was developed for the Bioconductor conferences. For more details, see the [Bioconductor Code of Conduct](https://www.bioconductor.org/about/code-of-conduct/)
7 |
8 |
9 | ## Social media policy
10 |
11 | Images and content from talks, workshops, and posters may be shared publicly through social media (Twitter, etc.). Videos will be released on the [Youtube Bioconductor channel](https://www.youtube.com/user/bioconductor). Please, inform the organizing committee as soon as possible if you don't wish your presentation material to be shared.
12 |
13 | ## The _Bioconductor_ conference aims to provide a supportive, collegial, and harassment-free environment
14 |
15 | _Bioconductor_ is dedicated to providing a supportive, collegial, and harassment-free
16 | conference experience for everyone, regardless of:
17 | * gender, gender identity and expression, sexual orientation, disability,
18 | physical appearance, body size, race, age, or religion.
19 | * intellectual position: approaches to data analysis, software preferences, coding style, scientific perspective, etc.
20 |
21 | The Virtual Event Code of Conduct applies to BioC 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.
22 |
23 | Conference participants violating these rules may be sanctioned or expelled from the conference with no refund,
24 | at the discretion of the conference organizers.
25 |
26 | ## Examples of unacceptable harassment, intimidation, and bullying behavior
27 |
28 | Harassment includes, but is not limited to:
29 |
30 | * Making comments in chats, to an audience or personally, that belittle or demean another person
31 | * Sharing sexual images online
32 | * Harassing photography or recording
33 | * Sustained disruption of talks or other events
34 | * Unwelcome sexual attention
35 | * Advocating for, or encouraging, any of the above behavior
36 |
37 | Intimidation and bullying include, but are not limited to:
38 |
39 | * Aggressive or browbeating behavior directed at someone during a public presentation
40 | * Mocking or insulting another person's intellect, work, perspective, or question/comment
41 | * Making reference to someone's gender, gender identity and expression, sexual orientation, disability,
42 | physical appearance, body size, race, age, religion, or other personal attributes in the context of a scientific
43 | discussion
44 | * Deliberately making someone feel unwelcome
45 |
46 | ### Enforcement
47 |
48 | Participants asked to stop any harassing behavior are expected to comply immediately.
49 |
50 | 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.
51 |
52 | 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.
53 |
54 | We expect participants to follow these rules at all event venues and event-related online activities.
55 |
56 | ### Reporting
57 |
58 | If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible.
59 | Harassment and other code of conduct violations reduce the value of our event for everyone.
60 | We want you to be happy at our event. People like you make our event a better place.
61 |
62 | You can make a report either personally or anonymously.
63 |
64 | #### Anonymous or Non-anonymous Report
65 |
66 | 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.
67 |
68 | 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.
69 |
70 | #### Personal Report
71 |
72 | You can make a personal report with any of the conference anti-harassment committee: Aedin Culhane, Levi Waldron, and Laurent Gatto.
73 |
74 | 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.
75 |
76 | 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.
77 |
78 | For Code of Conduct in other languages, see [bioc_coc_multilingual](https://kevinrue.github.io/bioc_coc_multilingual/)
79 |
80 | ### Code of Conduct violation reports
81 |
82 | * Email: [code-of-conduct@bioconductor.org](mailto:workshop@bioconductor.org?subject=BioC%20code-of-conduct)
83 | * Anonymous Code of Conduct violation reports: [https://tinyurl.com/bioccomplaint](https://tinyurl.com/bioccomplaint)
84 | * Law enforcement emergency number: 911 (US) / 112 (EU)
85 |
86 | ### Updates to the Code of Conducts
87 | [The Bioconductor Code of Conduct Committee](https://bioconductor.github.io/bioc_coc_multilingual/index.html) provide the most recent version of the Code of Conduct and translations in several languages.
88 |
89 | ### Code of Conduct Bioconductor Conference Committee
90 |
91 | | | | | | |
92 | |:-----:|---|:---:|---|:----:|
93 | |  | |  | |  |
94 | | [Aedin Culhane](mailto:aedin@jimmy.harvard.edu?subject=BioC%20code-of-conduct) | | [Levi Waldron](mailto:lwaldron.research@gmail.com?subject=BioC%20Code-of-conduct) | | [Laurent Gatto](mailto:laurent.gatto@uclouvain.be?subject=BioC%20Code-of-conduct) |
95 |
--------------------------------------------------------------------------------
/content/sponsors.md:
--------------------------------------------------------------------------------
1 |
146 |
147 |
148 |
149 |
150 |
151 | ## Sponsor Opportunities
152 | Bioconductor is a non-profit organization that supports one of the most widely used data analysis tools in genomics. Bioconductor was downloaded by [890,462 downloads (distinct IPs)](http://www.bioconductor.org/packages/stats/bioc/index.html) in 2021. Software packages are contributed by more than 1,200 community developers worldwide, totaling over half-million downloads per year.
153 |
154 | The conference is unique in that in addition to talks and poster session, the meeting features 20+ workshops which provide hands-on learning in Bioconductor. All conference materials (videos, slides, talks, posters, workshops) are published online such that the conference provides a rich resource for learning Bioconductor.
155 |
156 |
157 | > Interested in sponsoring this conference? Please contact
158 |
159 | **Your sponsorship will help increase diversity and representation at Bioconductor 2022** by:
160 |
161 | - Keeping registration costs affordable for academic participants and trainees.
162 | - Provide high quality hybrid/virtual programming and post-production and sharing of videos and conference materials
163 | - Funding travel scholarships for students and postdoctoral fellows.
164 | - Providing caregiver awards to assist in childcare or eldercare costs
165 | - Offering student diversity scholarships to increase participation of underrepresented minorities
166 |
167 | Three levels of sponsorship are available. Sponsors of all levels may present a poster highlighting the scientific interests of their organization in the poster sessions.
168 |
169 | **Platinum: $10,000 USD**
170 |
171 | - Poster session will be named after these donors.
172 | - Highest recognition, using your logo, in the online and print promotional and scheduling material.
173 | - Up to 8 free registrations.
174 | - A thank-you tweet including your preferred Twitter handle.
175 | - A virtual booth on the conference platform with the ability to set up live Q&A times and one-on-one meetings with attendees.
176 | - A virtual table during the poster session and social hours*
177 |
178 |
179 | **Gold: $5,000 USD**
180 |
181 | - Top recognition, using your logo, in the online and print conference promotional and scheduling material.
182 | - Up to 5 free registrations.
183 | - A thank-you tweet including your preferred Twitter handle.
184 | - A virtual booth on the conference platform with the ability to set up live Q&A times and one-on-one meetings with attendees.
185 | - A virtual table during the poster session and social hours*
186 |
187 | **Silver: $1,000 USD**
188 |
189 | - Sponsor names will be listed in the online and print promotional and scheduling material.
190 | - Academic discount on 2 registrations.
191 | - A thank-you tweet including your preferred Twitter handle.
192 |
193 | * Bioconductor will follow local and state guidelines and will only host in-person events if it is safe to do so.
194 |
195 | ***
196 |
197 | -->
216 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 |
2 | # Bioconductor conference template website
3 |
4 | This repository contains material for the Bioconductor annual conference.
5 | View the example at https://bioc2022.bioconductor.org/ and the corresponding
6 | [GitHub repo](https://github.com/Bioconductor/BioC2022)
7 |
8 | # Create a new website for an annual BiocConference
9 |
10 | ## Dependencies
11 |
12 | Make sure [Hugo is installed](https://gohugo.io/getting-started/installing/).
13 | Check Hugo version
14 |
15 | ```shell
16 | hugo version
17 | ```
18 |
19 | ## Branches
20 |
21 | - [master](https://github.com/Bioconductor/BioC_template/tree/master) branch contains a minimal set of files to create the conference website.
22 | - [master-full](https://github.com/Bioconductor/BioC_template/tree/master-full) contains additional files in subfolders [content/abstracts](https://github.com/Bioconductor/BioC_template/tree/master-full/content/abstracts), [content/news](https://github.com/Bioconductor/BioC_template/tree/master-full/content/news), [data/abstracts](https://github.com/Bioconductor/BioC_template/tree/master-full/data/abstracts) with additional files (mirror from the [BioC2022](https://github.com/Bioconductor/BioC2022) repository).
23 |
24 | ## Create a new repository
25 |
26 | 1. Create a new repository in https://github.com/Bioconductor using this
27 | template.
28 |
29 | 2. Clone the new repository and switch to it. For example:
30 |
31 | ```shell
32 | git clone git@github.com:Bioconductor/BioC_template.git
33 | cd BioC_template/
34 | ```
35 |
36 | 3. Edit the site
37 |
38 | - [config.toml](https://github.com/Bioconductor/BioC_template/tree/master/config.toml)
39 | - Adjust color style: style = "blue" (default), light-blue), green, marsala, pink, red, turquoise, violet
40 | - Edit "defaultKeywords", to make the site findable via Google. These keywords are used in `themes/hugo-universal-theme/layouts/partials/head.html`
41 | - .md files in the [content](https://github.com/Bioconductor/BioC_template/tree/master/content/) folder
42 | - .yaml files in [data/carousel](https://github.com/Bioconductor/BioC_template/tree/master/data/carousel/) (create a new hex logo, open an [issue](https://github.com/Bioconductor/BiocStickers/issues) on [BiocStickers](https://github.com/Bioconductor/BiocStickers/))
43 | - rename [data/committee.all](https://github.com/Bioconductor/BioC_template/tree/master/data/committee.all/) folder to `committee` and adjust committee members
44 | - add [data/speakers](https://github.com/Bioconductor/BioC_template/tree/master/data/speakers/)
45 | - add sponsors to [data/clients](https://github.com/Bioconductor/BioC_template/tree/master/data/clients/) and [static/img/clients](https://github.com/Bioconductor/BioC_template/tree/master/static/img/clients/) (take logos from [Google Drive]())
46 | - Edit the front page [news.html](https://github.com/Bioconductor/BioC_template/tree/master/layouts/partials/news.html)
47 |
48 | 4. Run Hugo to preview the webpage locally.
49 |
50 | ```shell
51 | rm -rf public; hugo --verbose; hugo server --disableFastRender --verbose
52 | ```
53 |
54 | View the results at http://localhost:1313/
55 |
56 | 5. Host your site on [Netlify](https://www.netlify.com/),
57 | as described [here](https://bookdown.org/yihui/blogdown/netlify.html).
58 | Use build command `hugo`, publish directory `public`,
59 | and set advanced variable `HUGO_VERSION` to your `hugo version` number,
60 | e.g., 0.105.0
61 |
62 | 6. To add an official URL/domain, e.g., bioc2023.bioconductor.org, first, contact [Lori](https://github.com/lshep) to create it. Second, login to Netlify, select the site, click "Domain settings" button, then "Add custom domain". Add the official URL when prompted and click "Verify". You'll get a message "bioconductor.org is already registered. If you registered this domain name through a different registrar, select Add subdomain to begin delegating it to Netlify." Click "Add subdomain", and the official domain will be added. Click "Check DNS configuration" and check how to update the CNAME recors. It'll take up to 24 hours before the changes will take effect.
63 |
64 | # Adding items to the schedule table
65 |
66 | 1. Make changes in the "schedule table" spreadsheet https://docs.google.com/spreadsheets/d/1tGtGffcbCRxQFjE3ej42IcWlN4FJCsuQeZvETt9g0oA/edit#gid=0. NOTE - For the "time" column, set the format to custom "hh:mm" (IMPORTANT)
67 | 2. Run the following command in the terminal in the base directory:
68 | ```bash
69 | Rscript --vanilla 1_create_yaml.R; bash 2_create_abstracts.sh; bash 3_create_tracks.sh
70 | ```
71 |
72 | ### Adding data for the schedule
73 |
74 | + Data for the abstracts and other elements for the schedule table should be located in `data/abstracts/`. This folder is populated by `1_create_yaml.R` from the "schedule table" spreadsheet.
75 |
76 | There are three types of abstracts.
77 |
78 | 1. papers. Name format: day1_1315_longWorkshop_paper25.yaml.
79 | 2. tracks. Name format: day1_0900_shortTalksSysEpi_track.yaml.
80 | 3. All other elements that will be added to the schedule.
81 |
82 | Abstract file name format: day[1-3]_HHMM_type_paper/track#.yaml.
83 | The abstracts should all contain these fields. If any field isn't used, it should remain blank.
84 |
85 | ```
86 | title: "" # A string with the full title.
87 | paper: "" # Number of paper or track. Valid options: paper# or track#. For example, paper2, track1, etc. track is only used for the short talks tracks. There is no defined track number as in the case of the papers, they should be added in order of appearance in the document.
88 | session_type: "" # String with the type. Valid options: "Short talk", "Short talks track", "Package demo", "Workshop".
89 | authors: "" # String with the authors separated by comma.
90 | presenting_author: "" # Author who will present. The first author by default.
91 | affiliation: "" # String with the affiliation.
92 | abstract: "" # String with the abstract. Sometimes there are quotes in the text which should be escaped.
93 | time: "" # The time in 24h format. Example: 1300 for 1 PM.
94 | github: "" # Haven't used this field. Not sure if this has been provided.
95 | twitter: "" # Twitter handle without the @.
96 | youtube: "" # Link to youtube video when available.
97 | day: "" # Valid options: day1, day2, day3.
98 | talks: "" # This field is only for the short talk tracks. This should list the number of papers under this track. This should be a YAML array. Example: ["paper10", "paper20"]
99 | ```
100 |
101 | + The `content/abstracts/` directory contains the individual pages for the
102 | abstracts. This directory could be ignored as it will be updated with
103 | the `2_create_abstracts.sh` and `3_create_tracks.sh` bash scripts. These scripts
104 | convert the elements in data to content pages.
105 |
106 | ======
107 |
108 | # data
109 |
110 | YAML files that need to be adjusted for each conference.
111 |
112 | ## abstracts
113 |
114 | YAML files for every event. `Workshop_paper` are processed by [content/workshops.md](content/workshops.md) and [layouts/shortcodes/workshops.html](layouts/shortcodes/workshops.html). All events are processed by [layouts/shortcodes/schedule.html](layouts/shortcodes/schedule.html).
115 |
116 | ## carousel
117 |
118 | YAML files for the carousel panels. Processed by the main theme.
119 |
120 | ## clients
121 |
122 | YAML files for sponsors. Processed by the main theme and [layouts/shortcodes/sponsors.html](layouts/shortcodes/sponsors.html)
123 |
124 | ## organizers
125 |
126 | YAML files for co-chairs and committee. Processed by [content/organizers.md](content/organizers.md), [layouts/shortcodes/cochairs.html](layouts/shortcodes/cochairs.html) and [layouts/shortcodes/committee.html](layouts/shortcodes/committee.html).
127 |
128 | ## speakers
129 |
130 | YAML files for each speaker. Processed by [layouts/partials/speakers.html](layouts/partials/speakers.html).
131 |
132 | # Disclaimer
133 |
134 | This template was created using the modified.
135 | [hugo-universal-theme](https://github.com/devcows/hugo-universal-theme).
136 | See the [demo web site](https://themes.gohugo.io/theme/hugo-universal-theme/),
137 | the original [github repository](https://github.com/devcows/hugo-universal-theme)
138 | and the [exampleSite files](https://github.com/devcows/hugo-universal-theme/tree/master/exampleSite).
139 | Template by [Bootstrapious](https://bootstrapious.com/p/universal-business-e-commerce-template).
140 | Ported to Hugo by [DevCows](https://github.com/devcows/hugo-universal-theme).
141 | The theme is added as selected files, not as a submodule, for easier modification.
--------------------------------------------------------------------------------
/content/workshops-status.md:
--------------------------------------------------------------------------------
1 |
2 | ## Workshops
3 |
4 | | Workshop | Source | Docker | Status |
5 | |:-------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
6 | | [Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment](https://stemangiola.github.io/bioc2021_tidytranscriptomics) | [](https://github.com/stemangiola/bioc2021_tidytranscriptomics) | [](https://hub.docker.com/r/stemangiola/bioc2021_tidytranscriptomics) | [](https://github.com/stemangiola/bioc2021_tidytranscriptomics/actions) |
7 | | [Dimension Reduction for Beginners](https://aedin.github.io/PCAworkshop) | [](https://github.com/aedin/PCAworkshop) | [](https://hub.docker.com/r/aculhane/pcabiocworkshop2020) | [](https://github.com/aedin/PCAworkshop/actions) |
8 | | [Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment](https://waldronlab.github.io/MultiAssayWorkshop) | [](https://github.com/waldronlab/MultiAssayWorkshop) | [](https://hub.docker.com/r/mr148/multiassayworkshop) | [](https://github.com/waldronlab/MultiAssayWorkshop/actions) |
9 | | [Effectively using the DelayedArray framework to support the analysis of large datasets](https://PeteHaitch.github.io/BioC2021_DelayedArray_workshop) | [](https://github.com/PeteHaitch/BioC2021_DelayedArray_workshop) | [](https://hub.docker.com/r/petehaitch/bioc2021_delayedarray_workshop) | [](https://github.com/PeteHaitch/BioC2021_DelayedArray_workshop/actions) |
10 | | [Introduction to Bioconductor annotation resources](https://jmacdon.github.io/Bioc2021Anno) | [](https://github.com/jmacdon/Bioc2021Anno) | [](https://hub.docker.com/r/jmacdon/bioc2021anno) | [](https://github.com/jmacdon/Bioc2021Anno/actions) |
11 | | [Reproducing a single-cell proteomics data analysis using QFeatures and scp](https://lgatto.github.io/QFeaturesScpWorkshop2021) | [](https://github.com/lgatto/QFeaturesScpWorkshop2021) | [](https://hub.docker.com/r/lgatto/qfeaturesscpworkshop2021) | [](https://github.com/lgatto/QFeaturesScpWorkshop2021/actions) |
12 | | [Trajectory inference across conditions: differential expression and differential progression](https://HectorRDB.github.io/bioc2021trajectories) | [](https://github.com/HectorRDB/bioc2021trajectories) | [](https://hub.docker.com/r/HectorRDB/bioc2021trajectories) | [](https://github.com/HectorRDB/bioc2021trajectories/actions) |
13 | | [systemPipe: Workflow and Visualization Toolkit](https://systemPipeR.github.io/systemPipeWorkshop2021) | [](https://github.com/systemPipeR/systemPipeWorkshop2021) | [](https://hub.docker.com/r/systempipe/systempipeworkshop2021) | [](https://github.com/systemPipeR/systemPipeWorkshop2021/actions) |
14 | | [Building Carpentries-based Bioconductor Lessons](https://jdrnevich.github.io/BuildACarpentriesWorkshop) | [](https://github.com/jdrnevich/BuildACarpentriesWorkshop) | [](https://hub.docker.com/r/jdrnevich/buildacarpentriesworkshop) | [](https://github.com/jdrnevich/BuildACarpentriesWorkshop/actions) |
15 | | [Epidemiology for Bioinformaticians](https://cmirzayi.github.io/epiforbioworkshop2021) | [](https://github.com/cmirzayi/epiforbioworkshop2021) | [](https://hub.docker.com/r/cmirzayi/epiforbioworkshop2021) | [](https://github.com/cmirzayi/epiforbioworkshop2021/actions) |
16 | | [Introduction to the Terra/AnVIL Cloud-based Genomics Platform](https://waldronlab.github.io/AnVILWorkshop) | [](https://github.com/waldronlab/AnVILWorkshop) | [](https://hub.docker.com/r/shbrief/anvilworkshop) | [](https://github.com/waldronlab/AnVILWorkshop/actions) |
17 |
18 |
19 |
20 | Find out more details on the [Workshops](/workshops) page!
21 |
--------------------------------------------------------------------------------
/config.toml:
--------------------------------------------------------------------------------
1 | baseurl = "/"
2 | title = "Bioconductor"
3 | theme = "hugo-universal-theme"
4 | # themesDir = "../.."
5 | languageCode = "en-us"
6 | # Site language. Available translations in the theme's `/i18n` directory.
7 | defaultContentLanguage = "en"
8 | # Enable comments by entering your Disqus shortname
9 | # disqusShortname = "devcows"
10 | # Enable Google Analytics by entering your tracking code
11 | # googleAnalytics = ""
12 |
13 | # Define the number of posts per page
14 | paginate = 50
15 |
16 | [menu]
17 |
18 | # Main menu
19 |
20 | [[menu.main]]
21 | identifier="home"
22 | name = "Home"
23 | url = "/"
24 | weight = 10
25 |
26 | [[menu.main]]
27 | identifier="schedule"
28 | name = "Schedule"
29 | url = "/schedule/"
30 | weight = 20
31 |
32 | #[[menu.main]]
33 | # identifier="Workshops"
34 | # name = "Workshops & demos"
35 | # url = "/workshops/"
36 | # weight = 21
37 |
38 | #[[menu.main]]
39 | # identifier="Package demos"
40 | # name = "Package demos"
41 | # url = "/package-demo/"
42 | # weight = 22
43 |
44 | [[menu.main]]
45 | identifier="Organizers"
46 | name = "Organizers"
47 | url = "/organizers/"
48 | weight = 20
49 |
50 | [[menu.main]]
51 | identifier = "about"
52 | name = "About"
53 | url = "#"
54 | weight = 60
55 |
56 | [[menu.main]]
57 | identifier="submissions"
58 | name = "Submissions"
59 | url = "/submissions/"
60 | weight = 30
61 |
62 | # [[menu.main]]
63 | # identifier="registration"
64 | # parent = "about"
65 | # name = "Registration"
66 | # url = "/registration/"
67 | # weight = 55
68 |
69 | #[[menu.main]]
70 | # identifier="workshops"
71 | # name = "Workshops"
72 | # url = "/workshops-status/"
73 | # weight = 4
74 |
75 | # https://github.com/devcows/hugo-universal-theme/issues/34
76 |
77 | [[menu.main]]
78 | identifier = "code"
79 | parent = "about"
80 | name = "Code of conduct"
81 | url = "/code/"
82 | weight = 8
83 |
84 | [[menu.main]]
85 | identifier = "conferences"
86 | parent = "about"
87 | name = "Past events"
88 | url = "/conferences/"
89 | weight = 9
90 |
91 | #[[menu.main]]
92 | # identifier = "conferences"
93 | # name = "Past events"
94 | # url = "/conferences/"
95 | # weight = 9
96 |
97 | # [[menu.main]]
98 | # identifier = "contact"
99 | # name = "Contact"
100 | # url = "/contact/"
101 | # weight = 8
102 |
103 | # Top bar social links menu
104 |
105 | [[menu.topbar]]
106 | weight = 1
107 | name = "GitHub"
108 | url = "https://github.com/Bioconductor/"
109 | pre = ""
110 |
111 | # [[menu.topbar]]
112 | # weight = 2
113 | # name = "Facebook"
114 | # url = "http://facebook.com"
115 | # pre = ""
116 |
117 | [[menu.topbar]]
118 | weight = 3
119 | name = "Twitter"
120 | url = "https://twitter.com/Bioconductor"
121 | pre = ""
122 |
123 | [[menu.topbar]]
124 | weight = 4
125 | name = "Email"
126 | url = "mailto:workshop@bioconductor.org"
127 | pre = ""
128 |
129 | [[menu.topbar]]
130 | weight = 5
131 | name = "Slack"
132 | url = "https://slack.bioconductor.org/"
133 | pre = ""
134 |
135 | [params]
136 | viewMorePostLink = "/blog/"
137 | author = "DevCows"
138 | defaultKeywords = ["Bioconductor Asia 2024", "Bioconductor Asia", "Bioconductor"]
139 | mainSections = ["blog"]
140 | # defaultDescription = "Site template made by devcows using hugo"
141 |
142 | # Social media
143 | facebook_site = "" # the Facebook handle of your site ('https://www.facebook.com/HANDLE')
144 | twitter_site = "Bioconductor" # the Twitter handle of your site (without the '@')
145 | default_sharing_image = "img/sharing-default.png"
146 |
147 | # Google Maps widget: If `googleMapsApiKey` is not set, no key will be passed to Google (which likely results in a broken map widget).
148 | enableGoogleMaps = false
149 | googleMapsApiKey = "AIzaSyCFhtWLJcE30xOAjcbSFi-0fnoVmQZPb1Y"
150 |
151 | latitude = "-12.043333"
152 | longitude = "-77.028333"
153 |
154 | # Style options: default (light-blue), blue, green, marsala, pink, red, turquoise, violet
155 | style = "green"
156 |
157 | # Since this template is static, the contact form uses www.formspree.io as a
158 | # proxy. The form makes a POST request to their servers to send the actual
159 | # email. Visitors can send up to a 1000 emails each month for free.
160 | #
161 | # What you need to do for the setup?
162 | #
163 | # - set your email address under 'email' below
164 | # - upload the generated site to your server
165 | # - send a dummy email yourself to confirm your account
166 | # - click the confirm link in the email from www.formspree.io
167 | # - you're done. Happy mailing!
168 | #
169 | # Enable the contact form by entering your Formspree.io email
170 | email = "your@email.com"
171 | contact_form_ajax = false
172 |
173 | about_us = "
Bioconductor Asia conference highlights current developments within and beyond the Bioconductor project.
185 | """
186 |
187 | [Permalinks]
188 | blog = "/blog/:year/:month/:day/:filename/"
189 |
190 | # Enable or disable top bar with social icons
191 | [params.topbar]
192 | enable = true
193 | text = """
Join/follow our community
194 |
195 |
196 |
197 | """
198 |
199 | # Enable and disable widgets for the right sidebar
200 | [params.widgets]
201 | categories = true
202 | tags = true
203 | search = false
204 |
205 | [params.carousel]
206 | enable = true
207 | # All carousel items are defined in their own files. You can find example items
208 | # at 'exampleSite/data/carousel'.
209 | # For more informtion take a look at the README.
210 |
211 | [params.features]
212 | enable = false
213 | # All features are defined in their own files. You can find example items
214 | # at 'exampleSite/data/features'.
215 | # For more informtion take a look at the README.
216 |
217 | [params.testimonials]
218 | enable = false
219 | # All testimonials are defined in their own files. You can find example items
220 | # at 'exampleSite/data/testimonials'.
221 | # For more informtion take a look at the README.
222 | title = "Testimonials"
223 | subtitle = "We have worked with many clients and we always like to hear they come out from the cooperation happy and satisfied. Have a look what our clients said about us."
224 |
225 | [params.speakers]
226 | enable = true
227 | # All testimonials are defined in their own files. You can find example items
228 | # at 'exampleSite/data/speakers'.
229 | # For more informtion take a look at the README.
230 | title = "Speakers"
231 | # subtitle = "Confirmed speakers"
232 |
233 | [params.see_more]
234 | enable = false
235 | icon = "far fa-file-alt"
236 | title = "Do you want to see more?"
237 | subtitle = "We have prepared for you more than 40 different HTML pages, including 5 variations of homepage."
238 | link_url = "#"
239 | link_text = "Check other homepages"
240 |
241 | [params.clients]
242 | enable = true
243 | # All clients are defined in their own files. You can find example items
244 | # at 'exampleSite/data/clients'.
245 | # For more informtion take a look at the README.
246 | title = "Our Sponsors"
247 | subtitle = ""
248 |
249 | [params.recent_posts]
250 | enable = false
251 | title = "From our blog"
252 | subtitle = "Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo."
253 |
254 | [markup.goldmark.renderer]
255 | unsafe= true
256 |
--------------------------------------------------------------------------------
45 | 
55 | 
"))
48 | docker_image_url <- sprintf("https://hub.docker.com/r/%s", x@docker)
49 | docker_link <- sprintf("[%s](%s)", docker_image, docker_image_url)
50 | status_badge <- sprintf("[](https://github.com/%s/actions)", x@github, x@badge, x@github)
51 | tibble::tibble(
52 | Workshop = workshop_link,
53 | Source = source_link,
54 | Docker = docker_link,
55 | Status = status_badge
56 | )
57 | })
58 | ```
59 |
60 | ```{r, include=FALSE}
61 | Paper9 <- Workshop(
62 | title = "Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment",
63 | github = "stemangiola/bioc2021_tidytranscriptomics",
64 | docker = "stemangiola/bioc2021_tidytranscriptomics",
65 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
66 | )
67 | Paper27 <- Workshop(
68 | title = "Dimension Reduction for Beginners",
69 | github = "aedin/PCAworkshop",
70 | docker = "aculhane/pcabiocworkshop2020",
71 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
72 | )
73 | Paper40 <- Workshop(
74 | title = "Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment",
75 | github = "waldronlab/MultiAssayWorkshop",
76 | docker = "mr148/multiassayworkshop",
77 | badge = "MAEWorkshopCheck/badge.svg"
78 | )
79 | Paper50 <- Workshop(
80 | title = "Effectively using the DelayedArray framework to support the analysis of large datasets",
81 | github = "PeteHaitch/BioC2021_DelayedArray_workshop",
82 | docker = "petehaitch/bioc2021_delayedarray_workshop",
83 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
84 | )
85 | Paper68 <- Workshop(
86 | title = "Introduction to Bioconductor annotation resources",
87 | github = "jmacdon/Bioc2021Anno",
88 | docker = "jmacdon/bioc2021anno",
89 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
90 | )
91 | Paper78 <- Workshop(
92 | title = "Reproducing a single-cell proteomics data analysis using QFeatures and scp",
93 | github = "lgatto/QFeaturesScpWorkshop2021",
94 | docker = "lgatto/qfeaturesscpworkshop2021",
95 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
96 | )
97 | Paper80 <- Workshop(
98 | title = "Trajectory inference across conditions: differential expression and differential progression",
99 | github = "HectorRDB/bioc2021trajectories",
100 | docker = "HectorRDB/bioc2021trajectories",
101 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
102 | )
103 | Paper81 <- Workshop(
104 | title = "systemPipe: Workflow and Visualization Toolkit",
105 | github = "systemPipeR/systemPipeWorkshop2021",
106 | docker = "systempipe/systempipeworkshop2021",
107 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
108 | )
109 | Paper112 <- Workshop(
110 | title = "Building Carpentries-based Bioconductor Lessons",
111 | github = "jdrnevich/BuildACarpentriesWorkshop",
112 | docker = "jdrnevich/buildacarpentriesworkshop",
113 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
114 | )
115 | Paper121 <- Workshop(
116 | title = "Epidemiology for Bioinformaticians",
117 | github = "cmirzayi/epiforbioworkshop2021",
118 | docker = "cmirzayi/epiforbioworkshop2021",
119 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
120 | )
121 | Paper124 <- Workshop(
122 | title = "Introduction to the Terra/AnVIL Cloud-based Genomics Platform",
123 | github = "waldronlab/AnVILWorkshop",
124 | docker = "shbrief/anvilworkshop",
125 | badge = ".github/workflows/basic_checks.yaml/badge.svg"
126 | )
127 | ```
128 |
129 | ```{r, echo=FALSE}
130 | workshop_table <- dplyr::bind_rows(
131 | renderTibbleRow(Paper9),
132 | renderTibbleRow(Paper27),
133 | renderTibbleRow(Paper40),
134 | renderTibbleRow(Paper50),
135 | renderTibbleRow(Paper68),
136 | renderTibbleRow(Paper78),
137 | renderTibbleRow(Paper80),
138 | renderTibbleRow(Paper81),
139 | renderTibbleRow(Paper112),
140 | renderTibbleRow(Paper121),
141 | renderTibbleRow(Paper124)
142 | )
143 | knitr::kable(workshop_table,
144 | format = "markdown",
145 | col.names = c("Workshop", "Source ", "Docker ", "Status"),
146 | align=c("l", "c", "c", "l")
147 | )
148 | ```
149 |
150 |