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
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆40Updated 4 years ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• cortes-ciriano-lab / ReConPlot
  ☆24Updated 11 months ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• deeptools / HiCMatrix
  ☆13Updated 3 months ago
• raphael-group / chisel
  CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
  ☆43Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 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
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• mccoy-lab / MAGE
  Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discover…
  ☆42Updated last year
• scoutzxb / CscoreTool
  ☆22Updated 5 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆35Updated 2 years ago
• adamewing / tebreak
  Find and characterise transposable element insertions
  ☆20Updated 2 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆26Updated 8 months ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 10 years ago
• js2264 / VplotR
  R package to easily generate "V-plots" of paired-end sequencing data over regions of interest
  ☆11Updated 2 years ago
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆42Updated 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
• homeveg / nuctools
  software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data
  ☆17Updated 6 years ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated last year
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆35Updated last year
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• dozmorovlab / multiHiCcompare
  Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.
  ☆10Updated 3 years ago
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆41Updated this week
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆52Updated 7 months ago