README.md

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

Documentation

Click here for the online documentation. This is a work in progress, still. If there is documentation that you'd like that doesn't exist, please make an issue report.

The "articles" link in the navbar at the top of the page has some vignettes that will help with some common tasks -- please do look at those, if you are a user of this package.

Installation and updating

The following will both install, and update if there are changes in the repository.

library(devtools)
# remove build_vignettes to save time
install_github("cmatKhan/brentlabRnaSeqTools", dependencies = TRUE)

# after you get the package installed, do this:
library(brentlabRnaSeqTools)

# if you think there are changes, but install_github disagrees, try using the argument force = TRUE

I have also installed this on my htcf cluster profile like so:

ml miniconda # note: this will definitely load, and most likely work as expected. But it does not come with a promise. It is a cluster module I wrote. If you have issues which you suspect to be a conda problem, I suggest that you install a version of miniconda in your home profile. It will be easier to address any conda related issues that way.

conda install -n brentlabRnaSeqTools # or whatever you want to call your env name

conda install r r-essentials libpq

$ R

> install.packages(devtools)
# YOU HAVE TO DO THIS! do not update RSQLite (as of 20210702 there is an install error in the boost/c++ package which is a dependency. You do not need to worry about this when you're installing)
> remotes::install_version("RSQLite", version = "2.2.5")
> install_github("cmatKhan/brentlabRnaSeqTools")

See the bamtools vignette for examples of how to use the functions to examine bam files in an Rscript that you could run with SLURM

uninstall

remove.packages("brentlabRnaSeqTools")

Singularity container

singularity pull library://cmatkhan/default/brentlab_rnaseq_tools:latest

issues

please do post issues to the issues tab. Please include the full error code and the command/context that lead to the error

to contribute

1. fork the repo
2. develop in a branch
3. create a pull request for the branch

This is the featureCounts/subreads homepage. In particular, has a good example of how to make mean/variance graph with voom http://bioinf.wehi.edu.au/RNAseqCaseStudy/

TODOs

• read more about packrat, add some instructions on how to use
• update R and dependencies to R version 4

brentlabRnaSeqTools

This is a very helpful tutorial on making an R package: https://tinyheero.github.io/jekyll/update/2015/07/26/making-your-first-R-package.html

this github post helped with installing bioconductor dependencies (deseq2 in this case): https://bioinformatics.stackexchange.com/a/3375

and this helped with installing from github: https://cran.r-project.org/web/packages/githubinstall/vignettes/githubinstall.html

Finally, here is a nice package development cheatsheet (for R): https://rawgit.com/rstudio/cheatsheets/master/package-development.pdf

cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.