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
  ☆23Updated last year
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆45Updated 3 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆40Updated 4 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆49Updated 3 years ago
• deeptools / HiCMatrix
  ☆13Updated 4 months ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆26Updated 10 months ago
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• cortes-ciriano-lab / ReConPlot
  ☆24Updated last year
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆53Updated 3 weeks ago
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• kundajelab / idr
  IDR
  ☆30Updated 2 years 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
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆42Updated 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 …
  ☆12Updated last month
• AndreasHeger / gat
  Genomic Association Tester
  ☆35Updated 2 years ago
• scoutzxb / CscoreTool
  ☆22Updated 5 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆74Updated 2 years ago
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated 2 years ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated last year
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆46Updated 6 months 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…
  ☆26Updated 9 months ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆63Updated 7 months ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆41Updated last year
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆57Updated last year
• adamewing / tebreak
  Find and characterise transposable element insertions
  ☆20Updated 2 years ago
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆24Updated this week