bedgraph

An R 📦 for fast and flexible DNA methylation analysis

A Python package for fast operations on 1-dimensional genomic signal tracks

Decode coverage.bedGraph files that use the run-length encoding format.

These scripts examine and display visual representations of .bedGraph and .bed files associated with CHIP-seq datasets.

FileIO.jl integration for bedGraph files

Computes per-sample coverage from multiple BAM, CRAM, or bedGraph files, ensuring each genomic position is counted only once per sample. Chromosomes are processed in parallel to maximize throughput, producing a single tabix-indexed bedGraph.gz file.

Read and write support for bedGraph file format.

Rust reimplementation of the MACS3 peak caller for ChIP-seq and ATAC-seq. Same CLI, byte-identical output, 2.3-4.9x faster.

Generate mappability tracks as BigWig file from genome fasta with GEM

A Shiny app for plotting bedgraphs on short sequences.

Region-subset bigWig / bedGraph track files for UCSC Genome Browser, igv.js and 3D Genome Browser. Underscore filenames, no Content-Encoding, mid-file HTTP Range verified 206.

Streaming, missing-aware bedGraph reconciliation with explicit tolerances, first-difference evidence, and deterministic CI reports.