PEER

bedGraphToBigWig converts bedGraph coverage files to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-seq, and WGBS coverage tracks.

1 shared topic • 1 shared operation

deepTools — suite of Python tools for efficient analysis and visualization of high-throughput sequencing data including ChIP-seq, ATAC-seq, MNase-seq, and RNA-seq. BAM-to-bigWig conversion with normal

1 shared topic • 1 shared operation

FusionCatcher — tool for detecting somatic fusion genes, translocations, and chimeric transcripts from RNA-seq data. Identifies known and novel gene fusions in tumor and normal samples using multiple

1 shared topic • 1 shared operation

PyDESeq2 — Python implementation of DESeq2 for differential gene expression analysis from bulk RNA-seq count data. Performs size factor normalization, genewise dispersion estimation, Wald tests with B

1 shared topic • 1 shared operation

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

1 shared topic • 1 shared operation