Man pages for e-myers/rnaseq
Process, Analyze and Visualize RNA-seq Data

bam_strand_splitSplit BAM with paired-end data into forward-strand and...
bamToBedConvert BAM files to bed format
bedgraph_flipConvert bedgraph values between positive and negative
bedgraphToBigWigBedgraph files to bigwig format
computeMatrixRead density per region
count_alignmentsGet alignment counts from BAM files
count_featuresRead in raw counts for genomic features
count_readsGet read counts from fastqs
counts_to_tpmGet transcripts per million
count_summariesGet read counts from featureCounts summary files
cutadapt_runTrim reads in fastq files
dir_checkCheck directory existence
exprHeatmapExpression heatmaps
exprLFCLog2 fold change heatmap
exprMeanMean expression heatmaps
featureCounts_runRead counts from BAM or SAM files
file_checksCheck file existence / extension
genomeCoverageBedBAM or bed files to bedgraph with histogram of coverage...
genomic_ranges_reduceReduce genomic ranges to set of non-overlapping ranges
get_exprGet counts or TPM matrix
helloHello, World!
plotHeatmapRead density per region - heatmap
sam_filterFilter SAM file
sam_to_bamSAM files filtered and converted to BAM format
STAR_runMap reads to genome
transcript_to_gene_fixReplace transcript ids with gene ids in GTF file
transcript_to_gene_mapCreate file associating transcript ids with gene ids
e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.