systemPipeR

Bioconductor package management and installation via BiocManager for R-based genomic data analysis. Install, update, and validate Bioconductor packages for RNA-seq, ChIP-seq, single-cell, methylation,

2 shared topics • 1 shared operation

Use when working with Borzoi — a sequence-to-function DNA foundation model — for predicting genome-wide regulatory activity from DNA sequences. Borzoi predicts RNA-seq, ATAC-seq, ChIP-seq, and histone

2 shared topics • 1 shared operation

GenomicRanges — Bioconductor R package for representing, manipulating, and analyzing genomic intervals (GRanges, GRangesList). Provides operations for finding overlaps (findOverlaps, subsetByOverlaps)

2 shared topics • 1 shared operation

Use when working with pybedtools — pybedtools — Python interface to BEDTools

2 shared topics • 1 shared operation

RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i

2 shared topics • 1 shared operation