Alternatives and similar repositories for HiChiP

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

• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆59Updated 3 years ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆60Updated 3 weeks ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆23Updated 3 months ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆65Updated last year
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆47Updated last week
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆43Updated 2 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆83Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated 11 months ago
• BioinfoUNIBA / REDItools2
  ☆58Updated 3 years ago
• LabTranslationalArchitectomics / riboWaltz
  optimization of ribosome P-site positioning in ribosome profiling data
  ☆52Updated 4 months ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆48Updated 2 years ago
• fansalon / TEspeX
  TEspeX - pipeline for Transposable Elements expression quantification
  ☆21Updated last year
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 3 months ago
• dovetail-genomics / Micro-C
  Micro-C QC and data analysis
  ☆16Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆48Updated 6 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
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆65Updated 6 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆18Updated 5 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆33Updated 3 years ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆109Updated 4 years ago
• Xinglab / espresso
  ☆61Updated 10 months ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 5 years ago
• ay-lab / mustache
  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
  ☆74Updated 5 months ago
• gaolabtools / scNanoGPS
  Single cell Nanopore sequencing data for Genotype and Phenotype
  ☆54Updated last month
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆46Updated 3 months ago