Man pages for uc-bd2k/GREP2
GEO RNA-Seq Experiments Processing Pipeline

build_indexBuild index for mapping using Salmon
get_fastqDownload fastq files
get_metadataDownload metadata from GEO and SRA
get_srrDownload SRA run files
process_geo_rnaseqA complete pipeline to process GEO RNA-seq data
run_fastqcQC report for each fastq files using FastQC
run_multiqcGenerate combined QC report for Salmon and FastQC
run_salmonQuantify transcript abundances using Salmon
run_tximportWrapper function to run tximport
trim_fastqTrim fastq files using Trimmomatic
uc-bd2k/GREP2 documentation built on Oct. 29, 2019, 5:15 a.m.