methylclock

MOABS (Model Based Analysis of Bisulfite Sequencing) — epigenomics toolkit for DNA methylation calling and differential methylation analysis from WGBS and RRBS experiments. Core tools: mcall (CpG meth

2 shared topics • 1 shared operation

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

Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH

1 shared topic • 1 shared operation

Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short

1 shared topic • 1 shared operation

g:Profiler — multi-organism functional enrichment analysis and gene identifier mapping toolkit. Performs over-representation analysis (ORA) against Gene Ontology (GO:BP, GO:MF, GO:CC), KEGG, Reactome,

1 shared topic • 1 shared operation