cooler

HiCExplorer — comprehensive toolkit for Hi-C chromosome conformation capture data analysis, quality control, normalization, and visualization. Provides hicBuildMatrix (contact matrix construction), hi

1 shared topic • 1 shared operation

SIP (Significant Interaction Peak caller) — Java-based tool for identifying chromosomal loops (significant interaction peaks) in Hi-C contact maps. Processes .hic (Juicebox), .mcool (cooler), or pre-p

1 shared topic • 1 shared operation

Use when working with STARR-seq (Self-Transcribing Active Regulatory Region sequencing) data analysis. STARRpeaker calls enhancer peaks from STARR-seq BAM files using negative binomial regression to a

1 shared topic • 1 shared operation

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

1 shared topic • 1 shared operation

WiggleTools — command-line toolkit for streaming arithmetic and set operations on genomic signal tracks stored in Wiggle, BigWig, BedGraph, and BAM/CRAM formats. Computes sums, means, products, log tr

1 shared topic • 1 shared operation