Open Chromosome Collective

All

28 repositories

.github
Public
MIT License
•0•0•0•0•Updated Feb 10, 2025Feb 10, 2025
bioframe
Public
Genomic interval operations on Pandas DataFrames
python bioinformatics genomics numpy pandas dataframes ngs-analysis genomic-ranges spatial-join genomic-intervals
Python
•
MIT License
•30•177•28•2•Updated Feb 10, 2025Feb 10, 2025
cooler
Public
A cool place to store your Hi-C
python bioinformatics genomics ngs file-format contact-matrix hdf5 sparse hi-c cooler
Python
•
BSD 3-Clause "New" or "Revised" License
•53•213•33•3•Updated Feb 10, 2025Feb 10, 2025
looplib
Public
A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.
Cython
•6•10•3•3•Updated Feb 10, 2025Feb 10, 2025
distiller-sm
Public
a Snakemake version of distiller - the Open2C Hi-C mapping workflow
bioinformatics snakemake bioinformatics-pipeline hi-c hic snakemake-workflow snakemake-pipeline
Python
•
MIT License
•3•4•8•0•Updated Jan 31, 2025Jan 31, 2025
pairtools
Public
Extract 3D contacts (.pairs) from sequencing alignments
python bioinformatics ngs hi-c 3d-genome file-formatter pairs-file
Python
•
MIT License
•32•107•41•5•Updated Jan 31, 2025Jan 31, 2025
polychrom-hoomd
Public
Python
•
MIT License
•4•7•0•0•Updated Jan 29, 2025Jan 29, 2025
open2c.github.io
Public
Welcome to the Open Chromosome Collective!
Ruby
•2•2•0•0•Updated Jan 20, 2025Jan 20, 2025
distiller-nf
Public
A modular Hi-C mapping pipeline
nextflow hi-c pipeline
Groovy
•
MIT License
•25•89•64•3•Updated Dec 5, 2024Dec 5, 2024
coolpuppy
Public
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
genomics contact-matrix hi-c sparse-matrix pileup python bioinformatics
Python
•
MIT License
•12•78•8•0•Updated Oct 31, 2024Oct 31, 2024
cooltools
Public
The tools for your .cool's
Jupyter Notebook
•
MIT License
•51•144•59•8•Updated Oct 21, 2024Oct 21, 2024
assemblyinfo
Public
Genome assembly metadata
Python
•
MIT License
•1•2•0•1•Updated Aug 12, 2024Aug 12, 2024
polykit
Public
Python
•
MIT License
•3•6•1•0•Updated Jul 30, 2024Jul 30, 2024
MultiQC
Public
Aggregate results from bioinformatics analyses across many samples into a single report.
JavaScript
•
GNU General Public License v3.0
•611•2•2•0•Updated Jul 21, 2024Jul 21, 2024
quaich
Public template
snakemake pipeline for Hi-C post-processing
hi-c workflow snakemake analysis
Python
•
MIT License
•6•22•7•0•Updated Jun 27, 2024Jun 27, 2024
gsoc
Public
Google Summer of Code - Open2C
0•0•0•0•Updated Mar 19, 2024Mar 19, 2024
open2c_examples
Public
Jupyter Notebook
•9•17•10•2•Updated Mar 12, 2024Mar 12, 2024
open2c_vignettes
Public
A collection of notebooks and gists demonstrating novel applications of open2c ecosystem of tools
Jupyter Notebook
•2•4•2•0•Updated Feb 7, 2024Feb 7, 2024
polychrom
Public
Chromosome polymer simulations and in silico capture experiments
polymer simulation hi-c chromatin chromosomes loop-extrusion
Python
•
MIT License
•16•47•9•2•Updated Dec 5, 2023Dec 5, 2023
inspectro-nf
Public
Python
•2•7•0•1•Updated Nov 23, 2023Nov 23, 2023
bioframe-poster
Public
https://open2c.github.io/bioframe-poster
Jupyter Notebook
•0•0•0•0•Updated Apr 14, 2023Apr 14, 2023
inspectro
Public
Hi-C spectral analysis workflow
Python
•2•7•2•0•Updated Apr 13, 2023Apr 13, 2023
pairtools-1
Public
CLI tools to process mapped Hi-C data
Python
•
MIT License
•32•1•0•0•Updated Sep 1, 2022Sep 1, 2022
pairlib
Public
Read, write and analyse Hi-C pairs
Python
•
MIT License
•0•3•4•0•Updated Apr 4, 2022Apr 4, 2022
MultiQC_TestData
Public
Test data for MultiQC. See https://github.com/ewels/MultiQC
HTML
•
MIT License
•145•0•0•0•Updated Dec 19, 2021Dec 19, 2021
cooler-binder
Public
Cooler demo using a Jupyter notebook Binder
Jupyter Notebook
•7•16•2•0•Updated Sep 24, 2020Sep 24, 2020
pyfilesplit
Public
Python
•
MIT License
•0•0•0•0•Updated Dec 21, 2018Dec 21, 2018
distiller-test-data
Public
Test data for distiller
Shell
•
MIT License
•0•0•0•0•Updated Jul 19, 2018Jul 19, 2018