Installation

Requirements

  • R 4.3 or newer.
  • Bioconductor packages: tximport, DESeq2, SummarizedExperiment, AnnotationDbi, fgsea, GSVA, and the annotation packages org.Hs.eg.db and org.Mm.eg.db.
  • CRAN packages: data.table and msigdbr.

rsemflow supports human and mouse data.

Option 1: install the R package from GitHub

Use this if you work in R, or on Windows without WSL.

install.packages("BiocManager")
BiocManager::install("DaikiKumakura/rsemflow")

BiocManager installs the CRAN and Bioconductor dependencies from the right repositories. The OrgDb annotation packages are optional dependencies; install them if you will use annotation ensembl:

BiocManager::install(c("org.Hs.eg.db", "org.Mm.eg.db"))

Option 2: install from source with the command-line launcher

On Linux, macOS, WSL, or an HPC login node, the installer also puts an rsemflow command on your PATH:

git clone https://github.com/DaikiKumakura/rsemflow.git
cd rsemflow
bash install_local.sh

The installer

  1. checks that R and Rscript are available;
  2. installs missing dependencies (scripts/install_dependencies.R);
  3. runs R CMD INSTALL .;
  4. links the launcher into $HOME/.local/bin (or $RSEMFLOW_BIN);
  5. runs rsemflow --version to confirm.

Options, set as environment variables:

Variable Effect
RSEMFLOW_BIN=/path/bin install the launcher somewhere else
RSEMFLOW_SKIP_DEPS=1 skip the dependency step (e.g. dependencies are managed by your cluster)

If $HOME/.local/bin is not on your PATH, add it (for example in ~/.bashrc):

export PATH="$HOME/.local/bin:$PATH"

Running the command line on Windows

Without WSL, call the same command-line interface through Rscript; everything after -e "rsemflow::cli_main()" is passed to rsemflow:

Rscript -e "rsemflow::cli_main()" data import --i-rsem-dir data --m-metadata metadata.tsv --o-study study

Check the installation

rsemflow --version
rsemflow --help

Then run the bundled example, which needs no annotation database or download:

bash inst/extdata/example/run_example.sh example-output

or, from R:

library(rsemflow)
ex <- system.file("extdata", "example", package = "rsemflow")
study <- read_rsem_study(file.path(ex, "data"), file.path(ex, "metadata.tsv"))
study

MSigDB gene sets

enrichment gsea and enrichment gsva use MSigDB through the msigdbr package unless you supply your own GMT file. Depending on your msigdbr version, the first use of a collection may download and cache data, so run it once on a machine with internet access. Custom GMT files (--i-genesets) need no download.

Troubleshooting

Message Cause and fix
rsemflow: command not found The launcher directory is not on PATH; see above.
R and Rscript must be on PATH Install R, or add its bin directory to PATH.
Annotation package 'org.Hs.eg.db' is not installed BiocManager::install("org.Hs.eg.db") (or org.Mm.eg.db).
Study format version ... is not supported The study was written by a different rsemflow version; run rsemflow data import again.