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
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆21Updated last year
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated 2 years ago
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated last year
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• vierstralab / genome-tools
  Processing and plotting tools for genomics data
  ☆21Updated 2 months ago
• paulsengroup / hictkpy
  Python bindings for hictk: read and write .cool and .hic files directly from Python
  ☆16Updated this week
• Xinglab / isoCirc
  isoCirc
  ☆10Updated last year
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆12Updated 4 years ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 4 years ago
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• mortazavilab / lapa
  Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
  ☆31Updated last year
• XiDsLab / TAGET
  ☆20Updated 3 years ago
• derijkp / scywalker
  A program for the analysis of single cell nanopore long read data
  ☆19Updated 3 months ago
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆67Updated last month
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 5 months ago
• BlanchetteLab / HIFI
  Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data
  ☆24Updated 3 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 7 months ago
• timplab / nanoNOMe
  nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis
  ☆19Updated 2 years ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• CSOgroup / CALDER2
  CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…
  ☆24Updated 6 months ago
• agalitsyna / RedClib
  Red-C data processing
  ☆15Updated 2 years ago