Alternatives and similar repositories for hictk:

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

• paulsengroup / hictkpy
  Python bindings for hictk: read and write .cool and .hic files directly from Python
  ☆14Updated last week
• 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 …
  ☆11Updated last year
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• XiaoTaoWang / StripeCaller
  A toolkit for analyzing architectural stripes
  ☆19Updated 4 months ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated last year
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆11Updated 3 years ago
• XiaoTaoWang / Best-Labs-of-3D-Genome
  Data and the co-authored network I extracted for lab selection in 3D genome research field
  ☆14Updated 3 years ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated 7 months ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆26Updated 3 years ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆41Updated 2 years ago
• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆21Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 9 months ago
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated last year
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆36Updated 3 weeks ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆38Updated 3 years ago
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated last year
• comprna / R2Dtool
  Analyse RNA feature distributions.
  ☆16Updated 4 months ago
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated 6 months ago
• CSOgroup / CALDER
  ☆21Updated last year
• sims-lab / CapCruncher
  Analysis tool for NG-Capture-C, Tri-C and Tiled-C data
  ☆9Updated 3 weeks ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆20Updated 3 years ago
• vierstralab / genome-tools
  Processing and plotting tools for genomics data
  ☆20Updated last month
• nvictus / lavaburst
  Chromatin domains bursting with flavor
  ☆12Updated 5 years ago
• smithlabcode / abismal
  Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
  ☆18Updated 2 months ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 4 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• broadinstitute / longbow
  Annotation and segmentation of MAS-seq data
  ☆20Updated last year
• bbglab / openvariant
  Read, parse and operate different multiple input file formats with OpenVariant
  ☆12Updated last week