BioC 2020: Where Software and Biology Connect

When: July 27 - 31, 2020
What: Community/Developer Day, Main Conference
Where: Virtual Conference
Slack: Bioconductor Team (#bioc2020 channel)
Twitter: #bioc2020

Workshops

Join the Bioconductor #bioc2020 and #bioc2020-workshops channels for up-to-date information.

100 Level Workshops

Workshop	Source	Docker
Introduction to Bioconductor annotation resources
A Tidy Transcriptomics introduction to RNA-Seq analyses
Public Data Resources in Bioconductor
Annotating inter-sample DNA methylation and ATAC-seq variation with COCOA
Human RNA-seq data from recount2 and related packages
Cloud-based Genomics using Terra/AnVIL
Epidemiology for Bioinformaticians Workshop

200 Level Workshops

Workshop	Source	Docker
Best practices for ATAC-seq QC and data analysis
Interactive Visualization of SummarizedExperiment Objects with iSEE
Functional enrichment analysis of high-throughput omics data
Copy number variation analysis with Bioconductor
MultiAssayExperiment and curatedTCGAData Bioconductor 2020 Workshop
CRISPRseek and GUIDEseq for designing target-specific gRNAs for the CRISPR genome editing system; Motif analysis with motifStack and dagLogo
Integrated ChIP-seq analysis workshop
An introduction to matrix factorization and principal component analysis in R
A workshop on discovering biomarkers from high through put response screens
Importing alevin scRNA-seq counts into R/Bioconductor

500 Level Workshops

Workshop	Source	Docker
Material on how to create and submit a package to Bioconductor
Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines in CWL
Effectively Using the DelayedArray Framework to Support the Analysis of Large Datasets
Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets
Trajectory inference across conditions: differential expression and differential progression
Efficient, Scalable, and Reproducible Enrichment Workflows

Workshops with preinstalled dependencies can be run locally using Docker.

• docker pull <userid/workshop:latest> will pull the latest image for a given <workshop>.
• docker run -e PASSWORD=<yourpassword> -p 8787:8787 -d --rm <userid/workshop> will publish a container’s port 8787 to the host (-p), run in the detached mode (-d), and cleanly remove the container when it is stopped (--rm).
• Open http://localhost:8787 and login with username rstudio and password <yourpassword>.
• Run browseVignettes(package = "<workshop>"). Click on one of the links, “HTML”, “source”, “R code”.
  • In case of “The requested page was not found” error, add help/ to the URL right after the hostname. This is a known bug.

Advanced: Use -v $(pwd):/home/rstudio argument to map your local directory to the container. Use -e DISABLE_AUTH=true, if you want passwordless login to RStudio. On Windows, you may need to provide your localhost IP address like http://191.163.92.108:8787/ - find it using docker-machine ip default in Docker’s terminal.

Example:

docker pull waldronlab/publicdataresources:latest
docker run -e PASSWORD=bioconductor -p 8787:8787 -d --rm waldronlab/publicdataresources
# Open http://localhost:8787 and login using rstudio/bioconductor credentials
# Run browseVignettes(package = "PublicDataResources")
# Open http://localhost:8787/help/library/PublicDataResources/doc/PublicDataResources.html
docker ps -a # List all running containers
docker stop <CONTAINER ID> # or, <NAMES> - Stop a container

Workshop packages were created using the BuildABiocWorkshop2020 template.

NOTE. All workshops should include a valid DESCRIPTION file with the following fields:

• URL: - the GitHub pages URL (https://username.github.io/repository)
• DockerImage: - the Docker repository slug in lowercase with (optional) tag (username/repository:tag)