Alternatives and similar repositories for hictk

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

• 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
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆22Updated last year
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated last year
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated 2 years ago
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆69Updated last week
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆39Updated last month
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆12Updated 4 years ago
• agalitsyna / RedClib
  Red-C data processing
  ☆15Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 4 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆39Updated last year
• timplab / nanoNOMe
  nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis
  ☆20Updated 3 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆49Updated 6 years ago
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• Xinglab / isoCirc
  isoCirc
  ☆10Updated 2 years ago
• paulsengroup / hictkpy
  Python bindings for hictk: read and write .cool and .hic files directly from Python
  ☆16Updated last week
• cortes-ciriano-lab / ReConPlot
  ☆24Updated 11 months ago
• guigolab / LyRic
  Long RNA-seq analysis workflow
  ☆21Updated last month
• rjdkmr / gcMapExplorer
  Genome Contact Map Explorer - gcMapExplorer. Visit:
  ☆21Updated 3 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆73Updated last year
• BlanchetteLab / HIFI
  Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data
  ☆24Updated 3 years ago
• nanoporetech / Pore-C-Snakemake
  ☆34Updated 2 years ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 5 years ago
• vierstralab / genome-tools
  Processing and plotting tools for genomics data
  ☆21Updated last week
• multiz / multiz
  DNA multiple sequence aligner, official version from Penn State's Miller Lab
  ☆36Updated 6 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 7 months ago
• XiaoTaoWang / StripeCaller
  A toolkit for analyzing architectural stripes
  ☆20Updated last year