Code and data reproducing results from "Visualizing the structure of RNA-seq expression data using grade of membership models", now published in PLoS Genetics.
View here to start browsing the R Markdown notebooks implementing the data analyses.
TO DO: Add a paragraph here giving a brief description of this repository, and what is contained in the repository. Refer to "repository organization" below for more details.
The R package corresponding to this work is CountClust. Check the
package details here.
TO DO: More details to add here in this section: (1) Link to Zenodo other resource(s) containing code and data relevant to PLoS Genetics paper, (2) Link to R package on Bioconductor, (3) give platform and software version(s) used to run the R code (e.g., Mac OS X, R and/or RStudio).*
If the data or code in this repository are useful for your research project, please cite the Zenodo resource, as well as our paper published in PloS Genetics:
Dey K, Hsiao C, and Stephens M (2017). Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genetics 13: e1006599
TO DO: Add licenses appropriate for code and for data/images; e.g., CC-BY and GPL.
TO DO: Give instructions here on installing software and downloading data in order to be able to run the R scripts/notebooks.
All documents related to this work are in the project folder. The
remaining folders contain files used to generate the webpages. The
project folder hosts several sub-directories---we list their
functionalities below:
project/src hosts the RMD scripts as well as the HTML outputs from
these files.
project/R hosts the R scripts, mostly scripts that run specific
analysis on data or derived data. Also includes scripts generating
figures for the paper.
project/plots hosts all the plots obtained by running the R and RMD
scripts.
project/rdas hosts the rda files storing lists or complex data
derived from running R/RMD scripts.
project/talks talks and presentations related to this project
project/docs current draft, submitted draft and bioRxiv draft of
the paper.
project/utilities hosts supplementary data - gene lists from the
analysis, gene annotations etc.
Please contact Kushal K Dey if you have any queries.