Alternatives and similar repositories for HiCtrans

Users that are interested in HiCtrans are comparing it to the libraries listed below

• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆22Updated last year
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 3 years ago
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆41Updated this week
• deeptools / HiCMatrix
  ☆13Updated 2 months ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆49Updated 6 years ago
• cortes-ciriano-lab / ReConPlot
  ☆23Updated 11 months ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago
• kundajelab / idr
  IDR
  ☆30Updated 2 years ago
• hoffmangroup / umap
  ☆30Updated 4 months ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated 2 years ago
• scoutzxb / CscoreTool
  ☆22Updated 5 years ago
• agalitsyna / fontanka
  Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …
  ☆12Updated 2 years ago
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated last year
• dozmorovlab / HiCcompare
  Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…
  ☆23Updated 2 years ago
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• js2264 / VplotR
  R package to easily generate "V-plots" of paired-end sequencing data over regions of interest
  ☆11Updated last year
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated 2 weeks ago
• Xinglab / rMATS-long
  ☆34Updated last week
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆12Updated 4 years ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆42Updated last year
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆98Updated last year
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆69Updated 2 months ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 10 years ago
• hiclib / pastis
  Poisson-based algorithm for stable inference of DNA Structure
  ☆39Updated last week
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆38Updated 8 months ago
• LappalainenLab / lorals
  ☆38Updated 2 years ago