📦 rsem

C

• convert-sam-for-rsem(1)Make a RSEM compatible BAM file.✨

R

• rsem-bam2wig(1)Convert BAM files to wiggle files.✨
• rsem-calculate-expression(1)Estimate gene and isoform expression from RNA-Seq data.✨
• rsem-control-fdr(1)Filter EBSeq output for statistical significance.✨
• rsem-generate-ngvector(1)Create Ng vector for EBSeq based only on transcript sequences.✨
• rsem-gff3-to-gtf(1)Convert GFF3 files to GTF files.✨
• rsem-plot-transcript-wiggles(1)Generate PDF wiggle plots from transcript or gene ids✨
• rsem-prepare-reference(1)Prepare transcript references for RSEM and optionally build BOWTIE/BOWTIE2/STAR/HISAT2(transcriptome) indices.✨
• rsem-run-ebseq(1)Wrapper for EBSeq to perform differential expression analysis.✨
• rsem-simulate-reads(1)Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.✨