Alternatives and similar repositories for pairsqc

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

• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated 2 years ago
• homeveg / nuctools
  software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data
  ☆17Updated 5 years ago
• scoutzxb / CscoreTool
  ☆21Updated 5 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• deWitLab / GENOVA
  GENome Organisation Visual Analytics
  ☆16Updated 3 years ago
• Xinglab / lr2rmats
  Long read to rMATS
  ☆32Updated 2 years ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆23Updated 4 years ago
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• dozmorovlab / HiCcompare
  Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…
  ☆22Updated 2 years ago
• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆21Updated last year
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆35Updated 9 months ago
• XiaoTaoWang / StripeCaller
  A toolkit for analyzing architectural stripes
  ☆20Updated 9 months ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 3 years ago
• plantformatics / Socrates
  ☆21Updated 6 months ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆51Updated 5 months ago
• Jfortin1 / TCGA_AB_Compartments
  A/B compartments for 12 cancer types estimated from TCGA methylation data
  ☆20Updated 8 years ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 10 years ago
• zhongw2 / GeneTEFlow
  ☆23Updated 4 years ago
• Xinglab / rMATS-long
  ☆32Updated 9 months ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆40Updated 3 years ago
• dozmorovlab / multiHiCcompare
  Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.
  ☆10Updated 3 years ago