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Table 1 Analysis tools for Hi-C data

From: Molecular and computational approaches to map regulatory elements in 3D chromatin structure

Software Function How to run Input Output
Distiller [163] Matrix generation Python package/Linux command line .fastq .mcool and .cool
HiCExplorer [214] Matrix generation Linux command line .sam, .bed .cool or .mcool
Hiclib [162] Matrix generation Linux command line .fastq .hdf5
HiC-Pro [160] Matrix generation Linux command line .bed .matrix
HiCUP [215] Matrix generation Linux command line .fastq .bam
HOMER [36] Matrix generation Linux command line/Mac/Windows .fastq .txt with matrix information, or .hic
Juicer [161] Matrix generation Linux command line .fastq .hic
TADbit [216] Matrix generation Python package/Linux command line .fastq, .dsrc .map
Arrowhead [141] TAD calling Linux command line .hic .bedpe
CaTCH [176] TAD calling R package .hic A list of data frame with domain information in R
Domaincaller (Directionaliy Index) [169] TAD calling Linux command line .cool .bed and .bedgraph
HiCDB [217] TAD calling R package/Linux command line with MATLAB N x N matrix, or K × 3 .txt
HiCseg [175] TAD calling R package Data in r matrix format List of t_hat, J, and t_est_mat data in R
HOMER [36] TAD calling Linux command line/Mac/Windows HiC tag directory from HOMER .2D.bed
TADbit [216] TAD calling Python package/Linux command line .bam or .map List of TADs in Python
TADCompare [218] TAD calling R package N x N matrix, x (N + 3) matrix, or 3-column matrix Data frame in R
TADPole [219] TAD calling R package Tab-separated matrix file TADpole object in R
TADtree [220] TAD calling Linux command line through Python script Contact matrix without column or row labels .txt files with three columns for contact domain information
TopDom [174] TAD calling R package Tab-separated matrix file with bin information .binsignal and.domain
3DNetMod [221] TAD calling Linux command line through Python script .bed and tab-separated matrix file Genomic coordinates and statistics output files 
FitHiC [179] Loop calling R pacakge/Linux command line with Python script Fragment file and interaction file .txt
FitHiC2 [180] Loop calling Linux command line Fragment file and matrix file .txt
GOTHiC [178] Loop calling R package .bam or bowtie2 alignment output Data frame in R
HiCCUPS [141] Loop calling Linux command line .hic .bedpe
HiC-DC [222] Loop calling Linux command line through R script File with Hi-C covariates and Hi-C counts File with data.table and fit information
HiCNormCis (FIREcaller) [223] Loop calling R package N x N matrices file Object in R
HOMER [36] Loop calling Linux command line/Mac/Windows HiC tag directory from HOMER .2D.bed
Mustache [182] Loop calling Linux command line .hic, .cool, or raw contact map with normalization vector .txt file and bias .txt file .tsv file with contact domain information and mustache scale
SIP [181] Loop calling Linux command line .hic, .mcool, or processed file with normalized value Loop file that can be loaded into Juicebox
StripeCaller [224] Loop calling Linux command line .cool .bedpe
HiCRep [184] Reproducibility testing R package Squared matrix, 3-column matrix, .hic or .cool Object in R
HiC-Spector [185] Reproducibility testing Linux command line for both Julia and Python implementation .hic or text delimited matrix file Reproducibility score
IDR2D [183] Reproducibility testing Linux command line .hic or .matrix and.bed from HiC-Pro IDR and significance value
FIND [187] Differential analysis R package Three column tab-separated file with matrix and four-column tab-separated file, or .hic Object in R
HiCCompare [186] Differential analysis R package .hic, .cool, or .matrix, and .bed from HiC-Pro Object in R
Selfish [188] Differential analysis Linux command line .hic, .cool, .bed, or .matrix Matrix of q-values in binary numpy file