Alternatives and similar repositories for HiCtool:

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

• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆39Updated 2 months ago
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• jsh58 / DMRfinder
  Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
  ☆27Updated last year
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆17Updated 5 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆31Updated 3 years ago
• ren-lab / hic-pipeline
  ☆24Updated 3 years ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆35Updated 3 years ago
• dixonlab / hic_breakfinder
  ☆36Updated 5 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated last year
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆37Updated 3 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆34Updated 3 months ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated last year
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated last year
• zhongmicai / Hic_tools_collection
  ☆11Updated 5 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 4 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆37Updated last year
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated 6 months ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆67Updated last year
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆34Updated 9 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆23Updated last week
• fansalon / TEspeX
  TEspeX - pipeline for Transposable Elements expression quantification
  ☆20Updated last year
• Xinglab / lr2rmats
  Long read to rMATS
  ☆31Updated last year
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆32Updated 2 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆57Updated 4 years ago
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆13Updated 11 months ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆20Updated 3 years ago