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
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
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