recount.rpkm.RData

This is the output of a pipeline that trains a Pathway-Level Information ExtractoR (PLIER) model on recount2 data (RPKM). See: https://github.com/greenelab/rheum-plier-data/tree/978c37938383ff7adcadacfcbc35931ce5e62b17<br><br>It was run in a Docker container. See the Github repository for more information. <br><br>Below, we include information about the scripts used to generate each item using the relative path from the repo top directory.<br><br>It contains:<br>* The rse-gene files downloaded from the recount bioconductor package (recount_experiments_rse-gene.tar.gz, output of recount2/1-get_all_recount_dataset.R)<br>* The RPKM normalized recount data (recount_rpkm.RDS, output of recount2/2-prep_recount_for_plier.R)<br>* The recount data processed for use with PLIER, the pathway data prepped for use with PLIER, and the k parameter for use with PLIER (recount_data_prep_PLIER.RDS, output of recount2/2-prep_recount_for_plier.R)<br>* The PLIER model itself (recount_PLIER_model.RDS, output of recount2/3-run_recount_plier.R)<br><br>If you use any of this data, please be sure to cite:<br><br>Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B and Leek JT (2017). "Reproducible RNA-seq analysis using recount2." Nature Biotechnology. doi: 10.1038/nbt.3838<br><br>And the PLIER preprint, if you use the PLIER model:<br><br>Mao W, Harmann B, Sealfon SC, Zaslavsky E, and Chikina M (2017). "Pathway-Level Information ExtractoR (PLIER) for gene expression data." bioRxiv. doi: 10.1101/116061<br><br>