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.
  ☆263Updated 6 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆239Updated this week
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆405Updated 3 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
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆67Updated 2 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 7 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated this week
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆207Updated 7 years ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 3 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated last month
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆328Updated 10 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated last month
• open2c / cooltools
  The tools for your .cool's
  ☆158Updated 6 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆199Updated this week
• GuyTeichman / RNAlysis
  Analyze your RNA sequencing data without writing a single line of code
  ☆140Updated 7 months 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
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆201Updated 3 weeks ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆251Updated this week
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆123Updated 3 months ago
• ENCODE-DCC / rna-seq-pipeline
  ☆157Updated 3 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆202Updated last week
• open2c / cooler
  A cool place to store your Hi-C
  ☆230Updated this week
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆205Updated last year
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆209Updated last week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆292Updated 2 months ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆335Updated last month
• saketkc / gencode_regions
  Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files
  ☆116Updated 4 years ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆493Updated last week
• gosling-lang / gos
  A declarative interactive genomics visualization library for Python.
  ☆233Updated last month
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆351Updated 3 weeks ago