xentrics/geo2rnaseq repository overview

⁠GEO2RNAseq: An easy-to-use R pipeline for complete pre-processing of RNA-seq data

RNA-seq pipeline developed in the research group Systems Biology and Bioinformatics⁠ at HKI⁠.

Cite: https://doi.org/10.1101/771063 ⁠

⁠Installation / Run

• GEO2RNAseq is available in
  • https://hub.docker.com/repository/docker/xentrics/geo2rnaseq⁠
  • https://singularity-hub.org/collections/4387⁠
  • [https://bitbucket.org/Xentrics/geo2rnaseq/src/master/](from⁠ source)
• Running vom Docker is the most easy way to use
  • it will run the R-studio server as supplied by rocker/rstudio⁠
    1. run the docker commands below
    2. in your browser, go to localhost:8787
    3. login as rstudio with the password you chose in the command

Minimum docker commands

docker pull xentrics/geo2rnaseq
docker run -d -p 8787:8787 -v $(pwd):/analysis -e PASSWORD=yourpasswordhere xentrics/geo2rnaseq

If you want to keep you current user ID and Group IDs for output files, the docker needs to be started differently:

docker run -d \
    -e PASSWORD=yourpasswordhere \
    -p :8787:8787 \
    -v $(pwd):/analysis \
    xentrics/geo2rnaseq \
    bash -c "groupadd -g $(id -g) GROUP ; \
            usermod -u $(id -u) -g $(id -g) -d /analysis rstudio && \
            /init"

⁠Features

• processing of RNA-seq raw data
  • for single RNA-seq, dual RNA-seq, and triple RNA-seq, e.g. host-pathogen interactions
  • for single-end, paired-end and mixed SE/PE sequencing
• for Linux and Mac
• Conda⁠ package

⁠Steps (most are optional)

• get raw data and metadata from GEO
• quality control
• quality and adapter trimming
• rRNA removal
• mapping
• counting
• mapping stats
• clustering, PCA
• DEG analysis with multiple tools
• visualization for each step

⁠Important Files and Folders

• R/ collection of functions
  • needed by the pipeline scripts
  • run R.utils::sourceDirectory("R/") to use GEO2RNA-seq without actually installing the package
• inst/extdata/pipelines/ actual RNA-seq pipelines for different types of datasets, application examples
• inst/extdata/BASH/ shell scripts to download raw and metadata from GEO
• inst/extdata/multiqc_config.yaml MultiQC⁠ example config file
• inst/doc/ detailed documentation (R vignette)

⁠Enhancing packages

biocLite(c(
    "airway",
    "IRanges",
    "TxDb.Dmelanogaster.UCSC.dm3.ensGene",
    "GEOquery",
    "pasillaBamSubset",
    "SRAdb"
))

install.packages(c(
    "dendextend",
    "roxygen2"
))

⁠Contact

[email protected]⁠