Count Rna-Seq Data Used For Benchmarking Fdr Control Methods

This submission contains three DESeqDataSet objects with RNA-seq count data.<br> <br> The files "rnaseq-brain-counts.rds" and "gsea-human-counts.rds" contain subsets of the GTEx data. These samples were downloaded using the Short Read Archive Toolkit and mapped to the human reference genome version GRCh38 using STAR v2.4.2a. htseq-count was used to tabulate the number of uniquely mapping reads for each gene. We used the DESeq2 format the data into DESeqDataSet objects. File "rnaseq-brain-counts.rds" contains 20 samples from two regions of the human basal ganglia, the nucleus accumbens and the putamen. FIle "gsea-human-counts.rds" contains 10 samples (6 cerebellum and 4 cortex samples). <br> <br> The file "gsea-human-counts.rds" contains RNA-seq count data from mouse hematopoietic stem cells and multipotent progrenitors (Cabezas-Wallscheid et al. Cell Stem Cell, 2014). The raw fastq data is available through the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-2262. These data were mapped to the mouse reference genome GRCm38 (ENSEMBL release 69) using the Genomic Short-Read Nucleotide Alignment program (version 2012-07-20). We used htseq-count to count the number of reads overlapping with each gene and used the DESeq2 package to format the data as a DESeqDataSet R object.