Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
pypi.org "hi-c" keyword
hicreppy 0.1.0
Reimplementation of the hicrep with added support for sparse matrix and multiple chromosomes.6 versions - Latest release: about 2 years ago - 1 dependent repositories - 94 downloads last month - 15 stars on GitHub - 1 maintainer
hicpeaks 0.3.7
A Python implementation for BH-FDR and HiCCUPS14 versions - Latest release: 9 months ago - 1 dependent repositories - 118 downloads last month - 38 stars on GitHub - 1 maintainer
Top 9.0% on pypi.org
130 versions - Latest release: 2 days ago - 1 dependent package - 4 dependent repositories - 1.67 thousand downloads last month - 35 stars on GitHub - 5 maintainers
hicstuff 3.2.3
General purpose stuff to generate and handle Hi-C data in its simplest form.130 versions - Latest release: 2 days ago - 1 dependent package - 4 dependent repositories - 1.67 thousand downloads last month - 35 stars on GitHub - 5 maintainers
tadlib 0.4.5
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains21 versions - Latest release: over 1 year ago - 1 dependent repositories - 225 downloads last month - 39 stars on GitHub - 2 maintainers
Top 6.1% on pypi.org
33 versions - Latest release: about 5 years ago - 5 dependent packages - 14 dependent repositories - 325 downloads last month - 81 stars on GitHub - 1 maintainer
pypairix 0.3.7
Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contain...33 versions - Latest release: about 5 years ago - 5 dependent packages - 14 dependent repositories - 325 downloads last month - 81 stars on GitHub - 1 maintainer
Top 7.0% on pypi.org
11 versions - Latest release: 23 days ago - 3 dependent packages - 4 dependent repositories - 322 downloads last month - 87 stars on GitHub - 2 maintainers
pairtools 1.1.0
CLI tools to process mapped Hi-C data11 versions - Latest release: 23 days ago - 3 dependent packages - 4 dependent repositories - 322 downloads last month - 87 stars on GitHub - 2 maintainers
hic2cool 1.0.1
Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (f...28 versions - Latest release: 6 months ago - 1 dependent package - 1 dependent repositories - 1.19 thousand downloads last month - 53 stars on GitHub - 4 maintainers
Top 2.1% on pypi.org
45 versions - Latest release: 8 months ago - 22 dependent packages - 64 dependent repositories - 3.6 thousand downloads last month - 189 stars on GitHub - 2 maintainers
cooler 0.9.3
Sparse binary format for genomic interaction matrices.45 versions - Latest release: 8 months ago - 22 dependent packages - 64 dependent repositories - 3.6 thousand downloads last month - 189 stars on GitHub - 2 maintainers
corigami 0.0.1
C.Origami: cell type-specific chromatin structure prediction.1 version - Latest release: over 1 year ago - 25 downloads last month - 50 stars on GitHub - 2 maintainers
trackc 0.0.17
trackc aims to produce beautiful genome tracks that are highly customizable13 versions - Latest release: 28 days ago - 1 dependent repositories - 88 downloads last month - 3 stars on GitHub - 2 maintainers
stripecaller 0.1.0
Automated Stripe Identification from contact matrix.1 version - Latest release: about 4 years ago - 1 dependent repositories - 29 downloads last month - 16 stars on GitHub - 1 maintainer
runhic 0.8.7
A easy-to-use Hi-C processing software supporting distributed computation25 versions - Latest release: over 1 year ago - 1 dependent repositories - 165 downloads last month - 48 stars on GitHub - 1 maintainer
pareidolia 1.2.0
Multi-sample change detection in Hi-C patterns17 versions - Latest release: about 2 years ago - 1 dependent repositories - 83 downloads last month - 8 stars on GitHub - 2 maintainers
pairliftover 0.2.1
Convert genomic coordinates of contact pairs from one assembly to another.7 versions - Latest release: over 1 year ago - 1 dependent repositories - 55 downloads last month - 56 stars on GitHub - 1 maintainer
mustache-hic 1.3.3
Mustache is a Hi-C analysis tool49 versions - Latest release: 12 days ago - 1 dependent repositories - 437 downloads last month - 53 stars on GitHub - 4 maintainers
metator 1.3.2
A pipeline for binning metagenomic datasets from metaHiC data.31 versions - Latest release: 6 months ago - 1 dependent repositories - 176 downloads last month - 20 stars on GitHub - 4 maintainers
instagraal 0.1.6
Large genome reassembly based on Hi-C data.6 versions - Latest release: about 5 years ago - 1 dependent repositories - 49 downloads last month - 34 stars on GitHub - 3 maintainers
hicshuffle 1.1.2
FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis12 versions - Latest release: 5 months ago - 1 dependent repositories - 46 downloads last month - 0 stars on GitHub - 1 maintainer
gcmapexplorer 1.0.30
A platform to visualize and analyze genome contact maps28 versions - Latest release: over 5 years ago - 1 dependent repositories - 430 downloads last month - 21 stars on GitHub - 1 maintainer
Top 4.9% on pypi.org
90 versions - Latest release: about 1 year ago - 2 dependent packages - 15 dependent repositories - 799 downloads last month - 34 stars on GitHub - 2 maintainers
clodius 0.20.1
Tile generation for big data90 versions - Latest release: about 1 year ago - 2 dependent packages - 15 dependent repositories - 799 downloads last month - 34 stars on GitHub - 2 maintainers
chess-hic 0.3.8
Quantitative comparison and automatic feature extraction for chromatin contact data.10 versions - Latest release: 10 months ago - 3 dependent repositories - 74 downloads last month - 26 stars on GitHub - 1 maintainer
libbiosmoother 1.5.1
On-the-fly processing of interactome data16 versions - Latest release: 8 days ago - 1 dependent package - 985 downloads last month - 0 stars on GitHub - 1 maintainer
biosmoother 1.5.1
On-the-fly processing and visualization of interactome data15 versions - Latest release: 8 days ago - 103 downloads last month - 4 stars on GitHub - 1 maintainer
serpentine 0.1.3
Serpentine binning package for Hi-C contact maps4 versions - Latest release: over 4 years ago - 1 dependent repositories - 29 downloads last month - 5 stars on GitHub - 3 maintainers
coolpuppy 1.1.0
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.23 versions - Latest release: 10 months ago - 1 dependent repositories - 200 downloads last month - 71 stars on GitHub - 2 maintainers
hiclift 1.0
Convert genomic coordinates of contact pairs from one assembly to another.1 version - Latest release: over 1 year ago - 26 downloads last month - 59 stars on GitHub - 1 maintainer
diffdomain-py3 0.2.2
DiffDomain can test the significant difference of TADs on chromatin.15 versions - Latest release: 6 months ago - 91 downloads last month - 10 stars on GitHub - 1 maintainer
chromosight 1.6.3
Detect loops (and other patterns) in Hi-C contact maps.55 versions - Latest release: over 1 year ago - 2 dependent repositories - 386 downloads last month - 55 stars on GitHub - 3 maintainers
daric 0.2.20
DARIC, a computational framework to find quantitatively differential compartments from Hi-C data15 versions - Latest release: 4 months ago - 1 dependent repositories - 61 downloads last month - 384 stars on GitHub - 1 maintainer
tadtool 0.84
Assistant to find cutoffs in TAD calling algorithms.18 versions - Latest release: over 1 year ago - 2 dependent repositories - 43 downloads last month - 43 stars on GitHub - 1 maintainer
cloops2 0.0.5
Loop-calling and peak-calling for sequencing-based interaction data, including related analysis u...3 versions - Latest release: 10 months ago - 1 dependent repositories - 49 downloads last month - 35 stars on GitHub - 1 maintainer
corigami-demo 0.0.1
C.Origami: cell type-specific chromatin structure prediction.1 version - Latest release: over 1 year ago - 8 downloads last month - 50 stars on GitHub - 1 maintainer
Related Keywords
genomics
17
bioinformatics
15
python
9
Hi-C
8
chromatin
7
3d-genome
7
contact-matrix
7
cooler
6
pairs
4
3c
4
contact
3
ngs
3
computational-biology
2
convolutional-neural-network
2
epigenetics
2
cell type-specific
2
prediction
2
deep learning
2
radicl-seq
2
interactome-sequencing
2
grid-seq
2
data-visualization
2
file-format
2
stripes
2
deep-learning
2
transformer
2
interaction
2
loops
2
peaks
2
chromatin-loops
2
tads
2
tad
2
4DN
2
liftover
2
hdf5
1
metagenomics
1
genome-assembly
1
scaffolding
1
pileup
1
qc
1
structural-similarity
1
comparative-genomics
1
chromatin-organisation
1
Genome Contact Map Explorer
1
Contact Map Explorer
1
3D Genome Organization
1
higlass
1
gehlenborglab
1
genomic-data-analysis
1
un-limited-resolution
1
trac-looping
1
rehoboam
1
next-generation-sequencing
1
montage
1
hichip
1
domains
1
differential-enriched-loops
1
clustering
1
cloops2
1
chromatin-interaction
1
chia-pet
1
bioinformatics-tool
1
3d-genome-visualization
1
visualization
1
Hi-Trac
1
loop-calling
1
peak-calling
1
3d-genome-browser
1
pattern-detection
1
r
1
differential
1
sparse-matrix
1
format
1
converter
1
contact-matrices
1
juicer
1
pairs-file
1
file-formatter
1
random-access
1
pypairix
1
c
1
bgzip
1
tabix
1
pairix
1
hierarchy
1
sub-TAD
1
AP
1
Preference
1
Aggregation
1
TAD
1
bioinformatics-pipeline
1
reproducibility
1
metagenomic-pipeline
1
metagenome-assembly
1
louvain-community-detection
1
micro-c
1
change-detection
1
chromosome-conformation-capture
1
arima
1
4d-nucleome-network
1