Alternatives and similar repositories for bioframe:

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

• open2c / cooltools
  The tools for your .cool's
  ☆147Updated 5 months ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆108Updated last month
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆79Updated 4 months ago
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆92Updated 3 months ago
• open2c / cooler
  A cool place to store your Hi-C
  ☆214Updated this week
• igvteam / igv-notebook
  Module for embedding igv.js in an IPython notebook
  ☆74Updated last month
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆239Updated 3 months ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• pachterlab / seqspec
  machine-readable file format for genomic library sequence and structure
  ☆119Updated last month
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆101Updated 4 months ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆198Updated 4 months ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated 3 weeks ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆96Updated last month
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆68Updated 8 months ago
• lmdu / pyfastx
  a python package for fast random access to sequences from plain and gzipped FASTA/Q files
  ☆277Updated 2 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆160Updated this week
• gosling-lang / gos
  A declarative interactive genomics visualization library for Python.
  ☆223Updated last month
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆139Updated 2 weeks ago
• genialis / RNAnorm
  Normalization of RNA-seq gene expression
  ☆85Updated last month
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆82Updated 3 years ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆233Updated 3 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…
  ☆115Updated last year
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆67Updated last year
• jeremymcrae / liftover
  liftover for python, made fast with cython
  ☆87Updated 3 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆68Updated last year
• nvictus / pybbi
  Python bindings to UCSC BigWig and BigBed library
  ☆32Updated last month
• 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…
  ☆86Updated last week
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆124Updated 4 years ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆60Updated last year