Ecosyste.ms: Repos

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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

Rocker4/TestPR
  • * setup.py

Size: 9.77 KB - Last synced: over 1 year ago - Pushed: almost 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

sagrudd/megrim
  • * setup.py

Size: 532 KB - Last synced: about 1 month ago - Pushed: over 3 years 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

Maycown/bioinformatics-turtu-challenge
  • * requirements.txt

Last synced: about 1 year 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

007gzs/test
  • * requirements.txt

Size: 1.6 MB - Last synced: 5 months ago - Pushed: 5 months 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