BioC Asia 2020

When: Oct 15 - 18, 2020
What: Main Conference
Where: Virtual Conference
Slack: Bioconductor Team (#biocasia2020 channel)
Twitter: #BioCAsia2020
WeChat: BioCAsia2020参会群

Workshops

Join the Bioconductor #biocasia2020 channel for up-to-date information.

Getting started

Access and launch workshops by clicking here.

Chinese (中文)

Workshop	Source	Docker
使用limma、Glimma和edgeR，RNA-seq数据分析易如反掌
Analysis and visualization of microbiome datasets using MicrobiotaProcess
An introduction to single-cell RNA-sequencing analysis in Bioconductor

English

Workshop	Source	Docker
trackViewer: Lollipop/Dandelion plots for methylation status and mutation data
Building a Bioconductor package
Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines in CWL
tidytranscriptomics: analysing single-cell and bulk RNA sequencing data following the tidy data paradigm
Hands-on experience to CiteFuse that consists of a suite of tools for the integration and the downstream analysis of CITE-seq data

Using workshop docker images locally

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)