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Package Usage: pypi: pyranges
GenomicRanges for Python.
117 versions
Latest release: 11 months ago
41 dependent packages
5,368 downloads last month
View more package details: https://packages.ecosyste.ms/registries/pypi.org/packages/pyranges
View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/pyranges%2Fpyranges
Dependent Repos 66
tzuni/starsolo_quant_analysis
Analysis of quantification in StarSolo- ==0.0.77 requirements.txt
Size: 3.29 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
alexpreynolds/filter-regions
Filter genomic regions by score and proximity- 0.0.117 poetry.lock
- >=0.0.117 pyproject.toml
- ==0.0.117 requirements.txt
Size: 31.1 MB - Last synced: 10 months ago - Pushed: about 1 year ago
uzh-dqbm-cmi/singularity_recipes
Singularity image with toolbox for scRNA-seq analysis including some useful R packages- * bioinformatics/dna_toolbox_requirements.txt
Size: 97.7 KB - Last synced: 2 months ago - Pushed: 2 months ago
Rohan-cod/vcf2fhir Fork of elimuinformatics/vcf2fhir
- >=0.0.96 requirements.txt
Size: 2.12 MB - Last synced: 16 days ago - Pushed: over 1 year ago
SebastianHollizeck/mismatchfinder
- * setup.py
Size: 251 KB - Last synced: 12 months ago - Pushed: almost 2 years ago
kipoi/kipoiseq
Standard set of data-loaders for training and making predictions for DNA sequence-based models.- ==0.0.77 requirements.txt
Size: 31.7 MB - Last synced: 22 days ago - Pushed: 22 days ago
elimuinformatics/vcf2fhir
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration- >=0.0.96 requirements.txt
Size: 2.1 MB - Last synced: 28 days ago - Pushed: over 1 year ago
fergsc/TALON Fork of mortazavilab/TALON
Technology agnostic long read analysis pipeline for transcriptomes- * setup.py
Size: 11.2 MB - Last synced: 7 months ago - Pushed: over 1 year ago
singleron-RD/CeleScope
Single Cell Analysis Pipelines- * requirements.txt
Size: 9.38 MB - Last synced: 3 days ago - Pushed: 3 days ago
fakedrtom/SVAFotate
- ==0.0.95 requirements.txt
Size: 678 MB - Last synced: 3 months ago - Pushed: 3 months ago
aertslab/pycisTopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.- * requirements.txt
Size: 33.2 MB - Last synced: 4 days ago - Pushed: about 1 month ago
aertslab/pycistarget
pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.- * requirements.txt
Size: 5.73 MB - Last synced: 4 days ago - Pushed: about 1 month ago
aertslab/scenicplus
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.- * requirements.txt
Size: 46.6 MB - Last synced: 4 days ago - Pushed: 12 days ago
iRNA-COSI/APAeval
Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples- * utils/apaeval/requirements.txt
- * utils/apaeval/setup.py
Size: 52.1 MB - Last synced: 24 days ago - Pushed: 4 months ago
cellular-genomics/cluster-paired-end-tags
Script to cluster Paired End Tags (PETs) from chromatin conformation capture (3C) experiments- ==0.0.84 requirements.txt
Size: 251 KB - Last synced: 7 months ago - Pushed: over 3 years ago
Akazhiel/Micropep
Pipeline to identify putative micropeptides from alignment BAM files.- >=0.0.85 setup.py
Size: 66.4 KB - Last synced: about 1 year ago - Pushed: over 3 years ago
databio/bedshift
Bedfile perturbation tool- * requirements/requirements-all.txt
Size: 728 KB - Last synced: about 1 month ago - Pushed: 6 months ago
wangyibin/TDGP
my 3D genome pipeline and scripts repository- * requirement.txt
Size: 1.71 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
mikecormier/mosdepth_region_vis
- * requirements.txt
Size: 4.06 MB - Last synced: 11 months ago - Pushed: about 3 years ago
med-team/pyranges
2D representation of genomic intervals and their annotations- * environment.yml
Last synced: over 1 year ago
dpeerlab/SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data- ==0.0.115 requirements.txt
- * setup.py
Size: 166 MB - Last synced: 22 days ago - Pushed: 22 days ago
phansol/gremlin
GREMLIN: Genomic REarrangements by Machine Learning-based INspection- ==0.0.89 codes/requirements.txt
Size: 379 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
mvinyard/cell-tools
Single-Cell Data Analysis Tools- >=0.0.113 setup.py
Size: 134 KB - Last synced: 6 days ago - Pushed: 4 months ago
pziarsolo/primer_explorer2
- * requirements.txt
Size: 424 KB - Last synced: 2 months ago - Pushed: almost 3 years ago
AlexShein/coronaviruses
Searching for interesting secondary structures in coronaviruses- ==0.0.77 requirements.txt
Size: 23.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
shahcompbio/alhenaloader
- * setup.py
Size: 284 KB - Last synced: 26 days ago - Pushed: about 2 months ago
jtenwolde/SCARV
Selective Constraint Against Rare Variants- * setup.py
Size: 233 KB - Last synced: 8 days ago - Pushed: over 2 years ago
nkran/guido-old
Guide designer with microhomology predictor for MMEJ- ==0.0.77 requirements.txt
Size: 166 KB - Last synced: 10 months ago - Pushed: about 3 years ago
PreMedKB/PAnno
PAnno is a Pharmacogenomics Annotation tool for clinical genomic testing.- * requirements.txt
Size: 67 MB - Last synced: 15 days ago - Pushed: over 1 year ago
GrantDaly/mitochondrial-alignments
- =0.0.96=pyh5e36f6f_0 requirements.txt
Size: 311 KB - Last synced: 5 months ago - Pushed: 5 months ago
FabrizioG202/Bootstrapping-Pipeline-Python-R
- ==0.0.117 bootstrapping/python/requirements.txt
Size: 172 MB - Last synced: 6 months ago - Pushed: almost 2 years ago
fiberseq/fibertools
- ==0.0.115 requirements.txt
Size: 1.88 MB - Last synced: 25 days ago - Pushed: 9 months ago
alexpreynolds/region-selection
Methods for filtering for high-scoring genomic intervals- >=0.0.115 region_selection_apr.egg-info/requires.txt
Size: 34.7 MB - Last synced: 30 days ago - Pushed: about 2 years ago
broadinstitute/varianteval
Python API to compare variant callsets.- * requirements.txt
Size: 27.4 MB - Last synced: 22 days ago - Pushed: almost 2 years ago
ABehal2020/chipseq-visualization
- ==0.0.62 back-end/requirements.txt
Size: 4.78 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
Uauy-Lab/IBSpy
Python library to identify Identical By State regions- * Pipfile
- ==0.0.115 requirements.txt
Size: 12.9 MB - Last synced: 15 days ago - Pushed: about 1 year ago
FHIR/genomics-operations
A public reference implementation of HL7 FHIR Genomics Operations (http://build.fhir.org/ig/HL7/genomics-reporting/operations.html)- ==0.0.115 utilities/requirements.txt
Size: 1.5 MB - Last synced: 8 days ago - Pushed: 9 days ago
fmicompbio/adv_singlecell_2022
Material for the "Advanced topics in single-cell analysis" course (2022 edition)- * containers/container_jupyter/day2_multi-omics/environment.yml
- * containers/container_rstudio/day2_multi-omics/environment.yml
- * containers/container_rstudio/day2_multi-omics/requirements.txt
Size: 274 MB - Last synced: 2 months ago - Pushed: about 2 years ago
YosefLab/epitome
Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility- >=0.0.104 requirements.txt
Size: 157 MB - Last synced: 5 months ago - Pushed: over 1 year ago
xindong95/SCRIP
SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-cell resolution based on scATAC-seq.- >=0.0.95 setup.py
Size: 45.2 MB - Last synced: 5 months ago - Pushed: 5 months ago
ML4GLand/EUGENe
Elucidating the Utility of Genomic Elements with Neural Nets- 0.0.117 poetry.lock
- ^0.0.117 pyproject.toml
Size: 108 MB - Last synced: 4 days ago - Pushed: about 1 month ago
shahcompbio/scgenome-deprecated
- * setup.py
Size: 131 MB - Last synced: 18 days ago - Pushed: about 2 months ago
liusy-jz/MRBIGR
Mendelian Randomization-Based Inference of Genetic Regulation- * requirements.txt
Size: 16.8 MB - Last synced: 7 months ago - Pushed: over 2 years ago
togop/3DPolyS-LE
3D Polymer Simulation with Loop Extrusion.- * requirements_dev.txt
- * setup.py
Last synced: 25 days ago
wdecoster/methplotlib
Plotting tools for nanopore methylation data- >=0.0.77 setup.py
Size: 7.43 MB - Last synced: 8 days ago - Pushed: 4 months ago
chrisbluemel/SPICE
Tool that utilizes FAS on entire sets of transcripts and uses the scoring to put differential transcript expression data into a functional context.- * setup.py
Size: 612 KB - Last synced: 3 months ago - Pushed: 10 months ago
iric-proteo/pps
Personalized proteome service- * Pipfile
- ==0.0.99 Pipfile.lock
Last synced: over 1 year ago
shirondru/PCGC_Challenge
- ==0.0.117 requirements.txt
Size: 68.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
jsobolew/mgr
- ==0.0.115 wandb/run-20230427_110614-mjlun0j5/files/requirements.txt
- ==0.0.115 wandb/run-20230427_110717-t9zpwv8j/files/requirements.txt
Size: 337 MB - Last synced: 3 months ago - Pushed: 3 months ago
docmab23/PharmCare
- ==0.0.117 requirements.txt
Size: 70.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
alexpreynolds/nearest-transcripts
Return nearest per-gene transcripts within N bases of some set of regions- >=0.0.117 requirements.txt
Size: 6.84 KB - Last synced: 10 months ago - Pushed: over 1 year ago
Sage-Bionetworks/Genie
Validation and processing of GENIE files- ==0.0.115 requirements.txt
Size: 3.62 MB - Last synced: 5 days ago - Pushed: 5 days ago
molgenis/asterix
Automated PGx pipeline- * requirements.txt
Size: 46 MB - Last synced: about 1 month ago - Pushed: about 2 months ago
nanoporetech/pore-c 📦
Pore-C support- ==0.0.71 requirements/conda-spec.txt
- ==0.0.71 requirements/dev.txt
- ==0.0.71 requirements/docs.txt
- ==0.0.71 requirements/testing.txt
- ==0.0.71 requirements.txt
Size: 2.3 MB - Last synced: 16 days ago - Pushed: over 1 year ago
wuqi21/CeleScope Fork of singleron-RD/CeleScope
Single Cell Analysis Pipelines- * requirements.txt
Size: 9.14 MB - Last synced: about 1 month ago - Pushed: 12 months ago
CAWarmerdam/asterix Fork of molgenis/asterix
Automated PGx pipeline- * requirements.txt
Size: 23.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
dburkhardt/pycisTopic Fork of aertslab/pycisTopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.- * requirements.txt
Size: 32.3 MB - Last synced: 2 months ago - Pushed: over 1 year ago
koonimaru/omniplot
Statistical analysis, clustering and visualinzing scientific data with hassle free- * omniplot.egg-info/requires.txt
- * requirements.txt
Size: 40.4 MB - Last synced: 4 days ago - Pushed: 2 months ago
ML4GLand/SeqData
Annotated sequence data- 0.0.117 poetry.lock
- ^0.0.117 pyproject.toml
Size: 1.14 MB - Last synced: 4 days ago - Pushed: about 1 month ago
gifford-lab/skipguide
Predictive model for CRISPR-Cas9 mediated Exon Skipping- <=0.0.67 setup.py
Size: 538 KB - Last synced: 2 months ago - Pushed: about 3 years ago
gifford-lab/skipguide-analysis
- ==0.0.67 environment.yml
Size: 29.7 MB - Last synced: 2 months ago - Pushed: about 3 years ago
fuxialexander/ES
- ==0.0.115 environment.yml
Size: 19.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
NVIDIA-Genomics-Research/GEPSi
GEPSi simulates phenotypes for GWAS data based on a range of conditions and biological assumptions.- ==0.0.95 requirements.txt
Size: 533 KB - Last synced: about 1 year ago - Pushed: about 2 years ago
skalermo/mbi-lab3
- ==0.0.117 requirements.txt
Size: 6.89 MB - Last synced: about 1 year ago - Pushed: about 2 years ago
skalermo/mbi_labs
- ==0.0.117 mbi_cw3/requirements.txt
Size: 9.81 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
LondheShubham153/vcf2fhir-retro
- * setup.py
Size: 859 KB - Last synced: about 1 year ago - Pushed: over 3 years ago
DineshRavindraRaju/Pharmcare
Prediction of PGx Variants from 23&me and Ancestry- ==0.0.117 environment.yml
- ==0.0.117 requirements.txt
Size: 7.74 MB - Last synced: about 1 year ago - Pushed: about 1 year ago
shouvikmani/cell-rank-atac-seq
Using ATAC-seq to inform directionality in single-cell trajectory inference- ==0.0.115 environment.yml
Size: 17 MB - Last synced: about 1 year ago - Pushed: about 2 years ago
HYsxe/PRINT
- ==0.0.120 code/requirements.txt
Size: 49.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago
gagneurlab/mtsplice
- ==0.0.78 environment.yml
Size: 54 MB - Last synced: 16 days ago - Pushed: over 2 years ago
mcgilldinglab/MATES
A Deep Learning-Based Model for Quantifying Transposable Elements in Single-Cell Sequencing Data- ==0.0.129 setup.py
Size: 75.6 MB - Last synced: 3 days ago - Pushed: 3 days ago
KellisLab/benj
benj benj benj- * setup.py
Size: 667 KB - Last synced: 3 days ago - Pushed: 3 days ago
naumanjaved/genformer
- ==0.0.111 requirements.txt
Size: 3.64 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
deepcell/mavropoulos_2022
- 0.0.117 pipeline/poetry.lock
- >=0.0.112 pipeline/pyproject.toml
Size: 1.32 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
mikecormier/ConSplice
Constrained Splicing python module- =0.0.92 requirements.txt
Size: 60.2 MB - Last synced: 11 months ago - Pushed: over 1 year ago
mikecormier/SVAFotate
Annotate Structural Variants with Population Allele Frequency Info- * requirements.txt
Size: 70.4 MB - Last synced: 11 months ago - Pushed: over 2 years ago
GenomicsNX/epitome Fork of YosefLab/epitome
Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility- >=0.0.84 requirements.txt
Size: 157 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago