Alternatives and similar repositories for SIP

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

• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆18Updated 2 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆31Updated this week
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆28Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆43Updated 2 years ago
• tjs23 / nuc_dynamics
  Particle dynamics and simulated annealing for chromosome structure calculation
  ☆29Updated last year
• 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 year
• ay-lab / selfish
  SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.
  ☆17Updated 2 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 3 years ago
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• Roy-lab / grinch
  GRiNCH: Graph-Regularized NMF and Clustering for Hi-C
  ☆9Updated last year
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• paulsengroup / hictkpy
  Python bindings for hictk: read and write .cool and .hic files directly from Python
  ☆15Updated last week
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated 8 months ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 11 months ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 3 years ago
• XiaoTaoWang / StripeCaller
  A toolkit for analyzing architectural stripes
  ☆19Updated 6 months ago
• JRowleyLab / HiCrayon
  Web-Application for the cross-visualization of HiC and ChIP-seq data.
  ☆18Updated 7 months 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
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆11Updated 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
• agalitsyna / RedClib
  Red-C data processing
  ☆15Updated 2 years ago
• satijalab / scChromHMM
  🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.…
  ☆28Updated 3 years ago
• zanglab / SICER2
  ☆22Updated 4 months ago
• hemberg-lab / MicroExonator
  Snakemake pipeline for microexon discovery and quantification
  ☆20Updated 5 months ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆29Updated 10 months ago
• bernardo-de-almeida / motif-clustering
  Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy
  ☆26Updated 2 years ago
• homeveg / nuctools
  software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data
  ☆17Updated 5 years ago