Alternatives and similar repositories for cooler

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

• open2c / cooltools
  The tools for your .cool's
  ☆157Updated 5 months ago
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆100Updated last year
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆259Updated 4 months ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆249Updated last week
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆238Updated 10 months ago
• open2c / bioframe
  Genomic interval operations on Pandas DataFrames
  ☆184Updated last week
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆120Updated last month
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆207Updated 2 months ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆201Updated 5 months ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆74Updated last year
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆207Updated 7 years ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated last year
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆120Updated last year
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 6 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆196Updated last week
• pachterlab / seqspec
  machine-readable file format for genomic library sequence and structure
  ☆125Updated 3 months ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆157Updated last month
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆174Updated last year
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆327Updated 8 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆289Updated last month
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆91Updated 3 years ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆182Updated this week
• bxlab / bx-python
  Tools for manipulating biological data, particularly multiple sequence alignments
  ☆159Updated 2 weeks ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆122Updated 2 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆246Updated last week
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆146Updated 2 years ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆128Updated 5 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week