Alternatives and similar repositories for pairix:

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

• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 2 months ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆55Updated 2 years ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 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
  ☆108Updated 4 years ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• parklab / ShatterSeek
  ☆68Updated last year
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆65Updated 5 years ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆111Updated 2 months ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆47Updated 6 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆61Updated last year
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆64Updated last year
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆65Updated 5 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated last year
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆68Updated last year
• LHentges / LanceOtron
  ☆27Updated 8 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆73Updated 2 years ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆59Updated last year
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆80Updated 3 months ago
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆84Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 5 months ago
• ygidtu / trackplot
  trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…
  ☆89Updated 3 weeks ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆71Updated 9 months ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆57Updated last month
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆56Updated last month
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆55Updated 2 years ago