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recount2_PLIER_data.zip (16.67 GB)
recount.rpkm.RData
Version 4 2018-03-30, 15:15
Version 3 2018-03-27, 17:14
Version 2 2018-03-27, 17:13
Version 1 2017-12-19, 16:19
dataset
posted on 2018-03-30, 15:15 authored by Qiwen HuQiwen Hu, Jaclyn TaroniJaclyn TaroniThis 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
It was run in a Docker container. See the Github repository for more information.
Below, we include information about the scripts used to generate each item using the relative path from the repo top directory.
It contains:
* 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)
* The RPKM normalized recount data (recount_rpkm.RDS, output of recount2/2-prep_recount_for_plier.R)
* 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)
* The PLIER model itself (recount_PLIER_model.RDS, output of recount2/3-run_recount_plier.R)
If you use any of this data, please be sure to cite:
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
And the PLIER preprint, if you use the PLIER model:
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
It was run in a Docker container. See the Github repository for more information.
Below, we include information about the scripts used to generate each item using the relative path from the repo top directory.
It contains:
* 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)
* The RPKM normalized recount data (recount_rpkm.RDS, output of recount2/2-prep_recount_for_plier.R)
* 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)
* The PLIER model itself (recount_PLIER_model.RDS, output of recount2/3-run_recount_plier.R)
If you use any of this data, please be sure to cite:
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
And the PLIER preprint, if you use the PLIER model:
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
