Ecosyste.ms: Repos

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Package Usage: pypi: vcfpy

Python 3 VCF library with good support for both reading and writing
25 versions
Latest release: over 1 year ago
10 dependent packages
2,878 downloads last month

View more package details: https://packages.ecosyste.ms/registries/pypi.org/packages/vcfpy

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/bihealth%2Fvcfpy

Dependent Repos 37

ahwagner/ohdsi_variants
extraction of variant concepts from the VICC metaKB
  • ==0.12.2 Pipfile.lock

Size: 344 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

jackwadden/lamprey
A Loop-Mediated Isothermal Amplification (LAMP) concatemer analysis, variant calling, and polishing tool
  • * requirements.txt

Size: 424 KB - Last synced: over 1 year ago - Pushed: over 1 year ago

bihealth/snappy-pipeline
SNAPPY Nucleic Acid Processing in Python
  • >=0.13.2 requirements/base.txt

Size: 7.57 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

sequana/sequana
Sequana: a set of Snakemake NGS pipelines
  • * requirements.txt

Size: 35.5 MB - Last synced: 23 days ago - Pushed: 3 months ago

cancervariants/metakb
Central repository for the VICC metakb web application
  • ==0.13.4 requirements-dev.txt
  • ==0.13.4 requirements.txt

Size: 14 MB - Last synced: 21 days ago - Pushed: 21 days ago

danmaclean/programming_with_python
  • ==0.13.4 requirements.txt

Size: 3.33 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

mrichters/pVACtools Fork of griffithlab/pVACtools
  • ==0.13.3 requirements.txt

Size: 357 MB - Last synced: 20 days ago - Pushed: 20 days ago

robertopreste/mitoviz
Python package to plot variants on the human mitochondrial genome.
  • ==0.12.1 requirements.txt

Size: 82.7 MB - Last synced: 8 days ago - Pushed: 9 days ago

mitoNGS/mtoolnote
Variant annotator for MToolBox.
  • ==0.12.1 requirements.txt

Size: 8.3 MB - Last synced: 11 days ago - Pushed: over 1 year ago

cancerit/vcf_flag_modifier
Python application to remove specific flags from VCF files
  • ==0.13.0 requirements.txt

Size: 40 KB - Last synced: 8 months ago - Pushed: about 3 years ago

jxtSamFrimpong/Oldway
a betway live roulette scrapper
  • ==0.13.3 requirements.txt

Size: 15.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

cancerit/CASM-Smart-Phase
Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)
  • ==0.13.0 python/requirements.txt

Size: 307 KB - Last synced: 8 months ago - Pushed: about 2 years ago

milescsmith/SQANTI3 Fork of ConesaLab/SQANTI3
Repository of SQANTI3 tool for Quality Control of Long-Read Defined Transcriptomes
  • 0.13.3 poetry.lock

Size: 56.7 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

jfnavarro/hla_pipeline
DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions
  • * setup.py

Size: 1.55 MB - Last synced: 8 months ago - Pushed: almost 3 years ago

dameyerdave/civicpy Fork of griffithlab/civicpy
A python interface for the CIViC db application
  • ==0.13.0 Pipfile.lock
  • * setup.py

Size: 70.3 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

hylkedonker/multitrack
Predicting immunotherapy efficacy using a multitrack representation of longitudinal ctDNA measurements.
  • * requirements.txt

Last synced: 7 months ago

bposzewiecka/PhaseDancerSimulator
  • ==0.13.3 requirements.txt

Size: 245 KB - Last synced: 11 months ago - Pushed: 11 months ago

cschin/Peregrine_dev 📦
  • ==0.12.1 py/setup.py

Size: 2.64 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago

griffithlab/VAtools
A set of tools to annotate VCF files with expression and readcount data
  • * setup.py

Size: 38.8 MB - Last synced: 12 days ago - Pushed: 4 months ago

BioML-CM/CreamMist
  • ==0.13.3 requirement.txt

Size: 52.7 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

griffithlab/civicpy
A python interface for the CIViC db application
  • ==0.13.0 Pipfile.lock
  • * setup.py

Size: 79 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

czbiohub-sf/cerebra 📦
A tool for fast and accurate summarizing of variant calling format (VCF) files
  • * requirements.txt
  • ==0.12.1 requirements_versioned.txt

Size: 164 MB - Last synced: 5 days ago - Pushed: over 1 year ago

IDEA-PRIO/VPMBench
  • ==0.13.3 setup.py

Size: 392 KB - Last synced: over 1 year ago - Pushed: over 2 years ago

bihealth/spliceai-wrapper 📦
Wrapper for Illumina SpliceAI that caches results
  • * requirements/base.txt

Size: 43 KB - Last synced: about 1 month ago - Pushed: over 1 year ago

mobidic/MPA
MoBiDiC Priorization Algorithm
  • >=0.13.4 setup.py

Size: 8.62 MB - Last synced: 23 days ago - Pushed: about 2 years ago

hylkedonker/bearclaw
  • * requirements.txt

Last synced: about 1 month ago

Sjonnie404/NeoPipeline
Cryptic Neo-antigen finder
  • =0.13.4=pypi_0 requirements.txt

Size: 17 MB - Last synced: 11 months ago - Pushed: over 1 year ago

bihealth/ngs-chew
Tasty, tasty, NGS!
  • * requirements/base.txt
  • * requirements.txt

Size: 149 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

eudesbarbosa/snappy-pipeline Fork of bihealth/snappy-pipeline
SNAPPY Nucleic Acid Processing in Python
  • >=0.13.2 requirements/base.txt

Size: 2.16 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

informationsea/python-docker
Docker image of Python with my favorite packages
  • ==0.13.3 requirements-freeze.txt

Size: 26.4 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

eudesbarbosa/cubi-tk Fork of bihealth/cubi-tk
CUBI Tooling for SODAR, VarFish et al.
  • * requirements/base.txt
  • * requirements.txt

Size: 827 KB - Last synced: over 1 year ago - Pushed: over 1 year ago

LaborBerlin/hum-cubi-tk-fork Fork of bihealth/cubi-tk
CUBI Tooling for SODAR, VarFish et al.
  • * requirements/base.txt
  • * requirements.txt

Size: 790 KB - Last synced: 3 months ago - Pushed: 3 months ago

khourhin/sequana Fork of sequana/sequana
Sequana: a set of Snakemake NGS pipelines
  • * requirements.txt

Size: 35.8 MB - Last synced: 2 months ago - Pushed: 2 months ago

cokelaer/sequana Fork of sequana/sequana
Sequana: a set of Snakemake NGS pipelines
  • * requirements.txt

Size: 35.5 MB - Last synced: 3 months ago - Pushed: 3 months ago

MoCoMakers/hack4nf-2022
  • ==0.13.4 challenge-1/requirements.txt

Size: 18.2 MB - Last synced: 21 days ago - Pushed: about 1 year ago

cancerit/hairpin-wrapper
Ease-of-use wrapper around Mathijs' Sanders AdditionalBamStatistics cruciform-DNA detection algorithm
  • ==0.13.4 requirements.txt

Size: 3.59 MB - Last synced: 8 months ago - Pushed: over 1 year ago

natir/h2g2
  • ==0.12.1 requirements.txt

Size: 13.7 KB - Last synced: 10 months ago - Pushed: over 4 years ago

007gzs/test
  • * requirements.txt

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

CanDIG/CanCOGen_synthetic_variant_data
  • ==0.13.2 requirements.txt

Size: 28.3 KB - Last synced: about 2 months ago - Pushed: over 3 years ago

CBR-Invicta/GPS
Personalized prediction of the secondary oocytes number after ovarian stimulation: a machine learning model based on clinical and genetic data
  • 0.13.5 poetry.lock
  • ^0.13.3 pyproject.toml

Size: 32.2 MB - Last synced: 27 days ago - Pushed: over 1 year ago

ga4gh/gk-pilot
A pilot implementation of GKS Work Stream specifications.
  • ==0.13.8 datasets/civic/requirements.txt
  • ==0.13.8 datasets/moa/requirements.txt

Size: 27.3 MB - Last synced: 10 days ago - Pushed: 10 days ago

MikeWLloyd/Python_DockerBuild
  • ==0.12.1 requirements.txt

Size: 12.7 KB - Last synced: about 2 months ago - Pushed: about 3 years ago

Layth17/pVACtools Fork of griffithlab/pVACtools
  • * setup.py

Size: 235 MB - Last synced: 3 months ago - Pushed: 3 months ago

giovanniquinones/cerebra Fork of czbiohub-sf/cerebra
A tool for fast and accurate summarizing of variant calling format (VCF) files
  • ==0.13.0 environment.yml
  • * requirements.txt
  • ==0.12.1 requirements_versioned.txt

Size: 164 MB - Last synced: 9 months ago - Pushed: almost 3 years ago

varfish-org/varfish-server
VarFish: comprehensive DNA variant analysis for diagnostics and research
  • ~=0.13.6 Pipfile
  • ==0.13.6 Pipfile.lock
  • ==0.13.6 docs_manual/requirements.txt

Size: 54.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

sellth/cubi-tk Fork of bihealth/cubi-tk
CUBI Tooling for SODAR, VarFish et al.
  • * requirements/base.txt
  • * requirements.txt

Size: 801 KB - Last synced: 9 months ago - Pushed: 9 months ago

brand-fabian/varfish-server Fork of bihealth/varfish-server
VarFish: comprehensive DNA variant analysis for diagnostics and research
  • * requirements/base.txt

Size: 45.9 MB - Last synced: 8 months ago - Pushed: almost 3 years ago

GenomicMedLab/variation-normalizer-manuscript
Issue tracker for Variation Normalizer manuscript work
  • ==0.13.6 requirements.txt

Size: 31.6 MB - Last synced: 5 months ago - Pushed: 5 months ago

sequana/fastqc
sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
  • 0.13.6 poetry.lock

Size: 2.36 MB - Last synced: 28 days ago - Pushed: about 1 month ago

EGA-archive/beacon2-ri-tools-v2
  • ==0.13.6 requirements.txt

Size: 25 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

sequana/depletion
Deplete Fastq files from human or other content
  • 0.13.6 poetry.lock

Size: 15.3 MB - Last synced: 3 months ago - Pushed: 6 months ago

sequana/revcomp
A simple utility to convert a bunch of input fastq files into their reverse complement
  • 0.13.6 poetry.lock

Size: 755 KB - Last synced: 2 months ago - Pushed: 2 months ago

sequana/bioconvert
convert files from one format to another using bioconvert
  • 0.13.6 poetry.lock

Size: 1.35 MB - Last synced: 15 days ago - Pushed: 2 months ago

WalhoutLab/WormClust
  • ==0.13.6 2_b_UnsupervisedApproach/requirements.txt

Size: 8.23 MB - Last synced: 5 months ago - Pushed: 5 months ago

CompEpigen/figeno
Tool for plotting sequencing data along genomic coordinates.
  • >=0.13.5 pyproject.toml

Size: 36.8 MB - Last synced: about 9 hours ago - Pushed: about 9 hours ago

gzhoubioinf/SourcePrediction_package
  • ==0.13.6 requirements.txt

Size: 30.5 MB - Last synced: 7 days ago - Pushed: 7 days ago

dxkeac/Neo_ML
  • ==0.13.6 requirements.txt

Size: 0 Bytes - Last synced: 4 months ago - Pushed: 4 months ago

aehrc/genomator
Privacy-hardened, hallucination-resistant synthetic data generator.
  • ==0.13.8 experiment_tools/requirements.txt

Size: 15.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

UnknownEquineCoderFH/bio-r
  • ==0.13.8 requirements.txt

Size: 10 MB - Last synced: 28 days ago - Pushed: 29 days ago

Jinhyun-Kim/geography_prediction
  • ==0.13.8 environment.yml

Size: 623 KB - Last synced: about 2 months ago - Pushed: about 2 months ago

griffithlab/pVACtools
  • * setup.py

Size: 356 MB - Last synced: about 3 hours ago - Pushed: about 9 hours ago