Alternatives and similar repositories for CoolBox

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

• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆261Updated 5 months ago
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆67Updated 2 years ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆238Updated 11 months ago
• open2c / cooltools
  The tools for your .cool's
  ☆157Updated 5 months ago
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆208Updated 7 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated 2 weeks ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆201Updated this week
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 6 months ago
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆406Updated 2 months ago
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆167Updated last month
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆395Updated last week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated 2 weeks ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆197Updated last week
• gosling-lang / gos
  A declarative interactive genomics visualization library for Python.
  ☆232Updated last month
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆100Updated last year
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆328Updated 9 months 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
• jrderuiter / pybiomart
  A simple pythonic interface to biomart.
  ☆57Updated 5 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
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆243Updated 6 months ago
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆84Updated 4 years ago
• r-bioinformatics / edgePy
  A Python implementation of edgeR for differential expression analysis
  ☆104Updated 6 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆290Updated last month
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆492Updated last month
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆333Updated 4 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆156Updated 3 years ago
• openvax / gtfparse
  Parsing tools for GTF (gene transfer format) files
  ☆122Updated 10 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆250Updated 3 weeks ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
  ☆184Updated last week