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Search results for python vcf
python
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vcf
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207 search results found
Hail
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905
Cloud-native genomic dataframes and batch computing
Samplot
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458
Plot structural variant signals from many BAMs and CRAMs
Igv Reports
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298
Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
Genomics_general
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279
General tools for genomic analyses.
Pygeno
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242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Kipoi
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222
Kipoi's model zoo API
Vcf2phylip
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216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Somaticseq
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185
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Hgvs
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142
HGVS variant name parsing and generation
Sigprofilerextractor
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132
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Gcp Variant Transforms
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114
GCP Variant Transforms
Clinvar
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108
This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
Easysfs
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108
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
Vcf Kit
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107
VCF-kit: Assorted utilities for the variant call format
Ngscheckmate
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106
Software program for checking sample matching for NGS data
Yhaplo
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98
Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men
Neopredpipe
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93
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
Pipeline Structural Variation
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87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Svim
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85
Structural Variant Identification Method using Long Reads
Cutevariant
⭐
85
A standalone and free application to explore genetics variations from VCF file
Parliament2
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83
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Snps
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82
tools for reading, writing, merging, and remapping SNPs
Tiledb Vcf
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79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
Svtyper
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78
Bayesian genotyper for structural variants
Vcfpy
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78
Python 3 library with good support for both reading and writing VCF
Neat Genreads
⭐
72
NEAT read simulation tools
Scoary
⭐
71
Pan-genome wide association studies
Vcf2gwas
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62
Python API for comprehensive GWAS analysis using GEMMA
Pyvcf
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58
A Variant Call Format reader for Python.
Vawk
⭐
53
An awk-like VCF parser
Selectiontools
⭐
53
Pipeline to take VCF through to Selection Analysis.
Sv2
⭐
50
Support Vector Structural Variation Genotyper
Vcf2db
⭐
50
create a gemini-compatible database from a VCF
Cyvcf
⭐
50
A fast Python library for VCF files leveraging Cython for speed.
Vembrane
⭐
50
vembrane filters VCF records using python expressions
Pypgx
⭐
49
A Python package for pharmacogenomics (PGx) research
Vcfstats
⭐
48
Powerful statistics for VCF files
Svviz2
⭐
46
for visual evaluation of read support for structural variation
Admixturepipeline
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46
A pipeline that accepts a VCF file to run through Admixture
Smash
⭐
43
Benchmarking toolkit for variant calling
Gvanno
⭐
43
Generic human DNA variant annotation pipeline
Csv2vcf
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41
🔧 Simple script in python to convert CSV files to VCF
Mutmap
⭐
40
MutMap pipeline to identify causative mutations responsible for a phenotype
Gtctovcf
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39
Script to convert GTC/BPM files to VCF
Nphase
⭐
39
Ploidy agnostic phasing pipeline and algorithm
Qtl Seq
⭐
39
QTL-seq pipeline to identify causative mutations responsible for a phenotype
Msmc Tools
⭐
39
Tools and Utilities for msmc and msmc2
Fuc
⭐
38
Frequently used commands in bioinformatics
Svclone
⭐
38
A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
Gor
⭐
37
GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.
Svjedi
⭐
36
SV genotyping with long reads
Strangervisions
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35
Problematicsites_sars Cov2
⭐
34
Vcardtools
⭐
34
Automatically fix, split, normalize, group and merge/deduplicate vCard and VCF files (even large ones).
Cycledash
⭐
34
Variant Caller Analysis Dashboard and Data Management System
Relernn
⭐
33
Recombination Landscape Estimation using Recurrent Neural Networks
Vcf_parser
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32
Simple vcf parser, based on PyVCF
Svafotate
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32
Introgression Detection
⭐
31
Sve
⭐
30
Browsevcf
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29
BrowseVCF is a web-based application and workflow to quickly prioritise disease-causative variants in VCF files.
Sccaller
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28
Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
Vcf2tsvpy
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27
Genomic VCF to tab-separated values
Phenix
⭐
27
Public Health England SNP calling pipeline.
Cerebra
⭐
26
A tool for fast and accurate summarizing of variant calling format (VCF) files
Rad_tools
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26
A collection of usefull tools for RAD or GBS data analysis
Svdb
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26
structural variant database software
Varsome Api Client Python
⭐
26
Example client programs for Saphetor's VarSome annotation API
Rapid
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25
Vcf2fasta
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25
Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file
Mergevcf
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25
Python package and routines for merging VCF files
Svv
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24
Stupid Simple Structural Variant View
Neoepiscope
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23
predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data
Unfazed
⭐
23
Unfazed by genomic variant phasing
Vapr
⭐
23
VAPr: A Python package for NoSQL variant data storage, annotation and prioritization
Svpv
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23
Structural Variant Prediction Viewer
Allbiotc2
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22
Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.
Samovar
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22
Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
Mushi
⭐
22
[mu]tation [s]pectrum [h]istory [i]nference
Tapes
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21
TAPES : a Tool for Assessment and Prioritisation in Exome Studies
Cmdbtools
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21
Command line tools for CMDB varaints browser
Pathoscore
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21
pathoscore evaluates variant pathogenicity tools and scores.
Forestqc
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21
Quality control on genetic variants from next-generation sequencing data using random forest
Iliad
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21
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
Vcfassoc
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20
perform genotype-phenotype-association tests on a VCF with logistic regression.
Checkvcf
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20
Sanity check Variant Call Format (VCF) files.
Vcfpytools
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20
vcf file manipulation
Vatools
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20
A set of tools to annotate VCF files with expression and readcount data
Vcf2fhir
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20
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Rnaindel
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20
Somatic indel discovery tool for tumor RNA-Seq data.
Covgen
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20
Creates a target specific exome_full192.coverage.txt file required by MutSig
Genome Server 21
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20
Serve your genotypes and phenotypes via an API for satoshis
Isafe
⭐
19
Pinpoints the mutation favored by selection
Helmsman
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19
highly-efficient & lightweight mutation signature matrix aggregation
Pynnotator
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19
This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.
Pdbio
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19
Pandas-based Data Handler for VCF, BED, and SAM Files
Samchain
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18
Vcf To 23andme
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18
Convert imputed DNA.Land VCF to 23andMe raw data format
Vcftidy
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18
normalize, left-align, trim, validate and clean VCF files
Haplotypo
⭐
17
This is the Haplotypo repository
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