hic2cool

CNVnator — read-depth (RD) based copy number variation (CNV) detection from whole-genome sequencing BAM/CRAM files. Partitions the genome into equal-size bins, computes normalized read-depth signals,

2 shared topics • 1 shared operation

FAN-C is a Python framework for analysis, visualization, and exploration of Hi-C and related chromatin conformation capture data. Provides a unified API for importing, processing, and analyzing Hi-C c

2 shared topics • 1 shared operation

hap.py (Haplotype Comparison Tools) — Python/C++ benchmarking toolkit from Illumina for comparing VCF files against a gold-standard truth set. Computes SNP and INDEL precision, recall, and F1-score fo

2 shared topics • 1 shared operation

HiC-Pro is an all-in-one pipeline for processing Hi-C sequencing data from raw FASTQ files to normalized contact matrices. Performs read alignment with Bowtie2, restriction-fragment assignment, valid-

2 shared topics • 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

2 shared topics • 1 shared operation