Open Chromosome Collective

All

28 repositories

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
•50•207•31•3•Updated Nov 18, 2024Nov 18, 2024
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
•28•175•28•2•Updated Nov 18, 2024Nov 18, 2024
.github
Public
MIT License
•0•0•0•0•Updated Nov 7, 2024Nov 7, 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
pairtools
Public
Extract 3D contacts (.pairs) from sequencing alignments
python bioinformatics ngs hi-c 3d-genome file-formatter pairs-file
Python
•
MIT License
•32•104•41•5•Updated Oct 22, 2024Oct 22, 2024
cooltools
Public
The tools for your .cool's
Jupyter Notebook
•
MIT License
•51•140•60•8•Updated Oct 21, 2024Oct 21, 2024
polychrom-hoomd
Public
Python
•
MIT License
•4•7•0•0•Updated Oct 20, 2024Oct 20, 2024
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 Oct 11, 2024Oct 11, 2024
open2c.github.io
Public
Welcome to the Open Chromosome Collective!
Ruby
•1•2•0•0•Updated Sep 26, 2024Sep 26, 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
•603•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
looplib
Public
A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.
Cython
•6•10•4•3•Updated Mar 12, 2024Mar 12, 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
distiller-nf
Public
A modular Hi-C mapping pipeline
nextflow hi-c pipeline
Groovy
•
MIT License
•24•87•63•3•Updated Dec 13, 2023Dec 13, 2023
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
•144•0•0•0•Updated Dec 19, 2021Dec 19, 2021
cooler-binder
Public
Cooler demo using a Jupyter notebook Binder
Jupyter Notebook
•7•15•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