esohkevin/esohkevin.github.io

esohinformatics

Size: 25.1 MB - Last synced: about 3 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

Aptivi/VisualCard

A .NET vCard parser with Android contacts2.db and MeCard support

Language: C# - Size: 3.56 MB - Last synced: about 10 hours ago - Pushed: about 11 hours ago - Stars: 2 - Forks: 0

bioSyntax/bioSyntax

Syntax highlighting for computational biology

Language: Shell - Size: 2.53 MB - Last synced: about 2 hours ago - Pushed: about 1 year ago - Stars: 247 - Forks: 30

alipirani88/snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

Language: Python - Size: 61.8 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 4 - Forks: 4

vmware-samples/validated-solutions-for-cloud-foundation

A companion repository for the VMware Validated Solutions for VMware Cloud Foundation.

Language: Python - Size: 14.9 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 21 - Forks: 5

ACEnglish/truvari

Structural variant toolkit for VCFs

Language: Python - Size: 98.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 287 - Forks: 47

bigbio/py-pgatk

Python tools for proteogenomics analysis toolkit

Language: Python - Size: 125 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 9 - Forks: 11

marcguery/varif

Variant filter

Language: Python - Size: 121 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

yassinedoghri/ClearWater-vCard

ClearWater permet d’importer une liste de contacts fournis au format vcf (vCard), d’effectuer des opérations dessus et d'exporter une nouvelle liste au format csv.

Language: JavaScript - Size: 53.7 KB - Last synced: 4 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

quinlan-lab/mendacity

language-agnostic testing for inheritance models

Language: Python - Size: 7.81 KB - Last synced: 4 days ago - Pushed: about 6 years ago - Stars: 2 - Forks: 2

mrueda/beacon2-ri-tools Fork of EGA-archive/beacon2-ri-tools

Beacon v2 Reference Implementation (Data ingestion tools) - Actively maintained by the original author

Language: Perl - Size: 7.78 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 0

juliawiggeshoff/VCFpytools

Assortment of VCF processing scripts

Language: Python - Size: 12.7 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

charite/jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)

Language: Java - Size: 23.6 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 54 - Forks: 38

varfish-org/varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research

Language: Python - Size: 54.7 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 40 - Forks: 11

SouthGreenPlatform/AgroLD_ETL

AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. AgroLD ETL is the Python packages developed to transform plant datasets in RDF. Packages are developped for data standards such as GFF,GAF, VCF and specific plant databases.

Language: Python - Size: 1.81 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 1

tjparnell/biotoolbox

Tools for querying and analysis of genomic data

Language: Perl - Size: 7.34 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 27 - Forks: 16

py-vobject/vobject Fork of skarim/vobject

A full-featured Python package for parsing and creating iCalendar and vCard files

Language: Python - Size: 1.41 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 12 - Forks: 3

mhkarimi1383/ListToContact-VCF-

This Project convert number list to vcf files (First Names list and Family Names list are optical).

Language: C# - Size: 45.9 KB - Last synced: 7 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

JDoades/ConvertFrom-Vcf Fork of dmarkle/ConvertFrom-Vcf

Convert VCF Contact files into a CSV which is compatible with Outlook on the Web (OWA)

Language: PowerShell - Size: 19.5 KB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

gorpipe/gor

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.

Language: Java - Size: 12.8 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 37 - Forks: 13

kfarleigh/PopGenHelpR

PopGenHelpR is an R package that estimates commonly used population genomic statistics and generates publication quality figures.

Language: R - Size: 13.4 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 3 - Forks: 0

starskyzheng/panpop

Application of pan-genome for population

Language: Perl - Size: 62 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 64 - Forks: 7

anand-imcm/get-variant-info

A WDL-based workflow for extraction of variants and their associated info from large VCF files

Language: Python - Size: 56.6 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

jpenrici/Miscellaneous

Miscellaneous code: C++, Python, Bash, Portugol, Visualg ...

Language: Portugol - Size: 4.26 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 2 - Forks: 0

TRON-Bioinformatics/vafator

Annotate variants in a VCF file with technical annotations from one or more BAMs

Language: Jupyter Notebook - Size: 60.3 MB - Last synced: 7 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 0

rutgerkirkels/vcard-generator

Vcard generator library for PHP

Language: PHP - Size: 22.5 KB - Last synced: 11 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

moka-guys/dx_api_bridge

DNAnexus API bridge. Retrieve data object URIs. Manage archival processes and perform cost audits.

Language: Python - Size: 69.3 KB - Last synced: 12 days ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

FolkerKinzel/VCards

.NET library for reading, writing, and converting VCF files that comply with vCard standards 2.1, 3.0 and 4.0

Language: C# - Size: 85.9 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 13 - Forks: 4

harish2704/online-group-vcf-file-generator

A simple online tool to generate VCF contact from excel / csv with custom prefix / suffix etc

Language: Vue - Size: 10.7 KB - Last synced: 13 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

TileDB-Inc/TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Language: C++ - Size: 33 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 79 - Forks: 13

varfish-org/varfish-cli

VarFish REST API client (CLI + Python package)

Language: Python - Size: 356 KB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 2 - Forks: 3

xuan13hao/data_analysis

Bioinformatic data analysis scripts and pipelines

Language: Jupyter Notebook - Size: 43.8 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 2 - Forks: 0

aehrc/VariantSpark

machine learning for genomic variants

Language: JavaScript - Size: 74.5 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 138 - Forks: 44

USDA-VS/vSNP

vSNP -- validate SNPs

Language: Python - Size: 68.5 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 18 - Forks: 12

samtools/htslib

C library for high-throughput sequencing data formats

Language: C - Size: 12.2 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 769 - Forks: 443

pwwang/vcfstats

Powerful statistics for VCF files

Language: Python - Size: 1.69 MB - Last synced: about 10 hours ago - Pushed: 7 months ago - Stars: 54 - Forks: 17

jslfree080/bamscope

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)

Language: Java - Size: 207 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 0

brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

Language: Cython - Size: 14.7 MB - Last synced: 7 days ago - Pushed: about 2 months ago - Stars: 357 - Forks: 70

isinaltinkaya/vcfgl

Genotype likelihood simulator for VCF/BCF files

Language: C++ - Size: 85.1 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 5 - Forks: 1

OpenMendel/VCFTools.jl

Julia utilities for handling VCF files

Language: Julia - Size: 2.48 MB - Last synced: 18 days ago - Pushed: 25 days ago - Stars: 18 - Forks: 4

varfish-org/seqrepo-rs

A port of biocommons/seqrepo to the Rust programming language

Language: Rust - Size: 125 KB - Last synced: 19 days ago - Pushed: 27 days ago - Stars: 3 - Forks: 1

aprilweilab/picovcf

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

Language: C++ - Size: 151 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 6 - Forks: 0

Zilong-Li/vcfpp

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

Language: C++ - Size: 1.8 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 18 - Forks: 3

Astrotomic/laravel-vcard

A fluent builder class for vCard files.

Language: PHP - Size: 199 KB - Last synced: 13 days ago - Pushed: 3 months ago - Stars: 44 - Forks: 14

rasmushenningsson/VariantCallFormat.jl

Read and write VCF and BCF files

Language: Julia - Size: 917 KB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 11 - Forks: 3

AndersenLab/VCF-kit

VCF-kit: Assorted utilities for the variant call format

Language: Python - Size: 10.9 MB - Last synced: 19 days ago - Pushed: 8 months ago - Stars: 117 - Forks: 25

kelseykm/vcard4

An RFC 6350 compliant JavaScript library (with TypeScript type declarations) for generating and parsing version 4.0 vCards. Can also generate RFC 6351 compliant XML vCards and RFC 7095 compliant jCards.

Language: JavaScript - Size: 5.96 MB - Last synced: 22 days ago - Pushed: 6 months ago - Stars: 44 - Forks: 6

tariqdaouda/pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Language: Python - Size: 10.6 MB - Last synced: 9 days ago - Pushed: 7 months ago - Stars: 307 - Forks: 52

robertopreste/HmtNote 📦

Human mitochondrial variants annotation using HmtVar.

Language: Python - Size: 452 KB - Last synced: 11 days ago - Pushed: 6 months ago - Stars: 16 - Forks: 1

talk2bryan/vcf-generator

A simple VCF generator using random data

Language: Python - Size: 63.5 KB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

Language: Java - Size: 109 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 271 - Forks: 244

juliawiggeshoff/singularity-recipes

Recipes for Singularity

Size: 26.4 KB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 1 - Forks: 0

MRCIEU/pygwasvcf

Python library for reading GWAS summary statistics in GWAS-VCF files

Language: Python - Size: 58.6 KB - Last synced: 24 days ago - Pushed: about 2 years ago - Stars: 6 - Forks: 4

m7m0od/v-card

Electronic business card, containing contacts details and social profiles, you can create as many business cards as you want, with different information on each card .

Language: PHP - Size: 2.36 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

apriha/snps

tools for reading, writing, merging, and remapping SNPs

Language: Python - Size: 1.95 MB - Last synced: 16 days ago - Pushed: about 2 months ago - Stars: 88 - Forks: 18

elimuinformatics/vcf2fhir

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration

Language: Python - Size: 2.1 MB - Last synced: about 11 hours ago - Pushed: about 1 year ago - Stars: 36 - Forks: 23

BioInterchange/Ontologies

Home of the Genomic Feature and Variation Ontology (GFVO)

Language: Ruby - Size: 738 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 16 - Forks: 4

polykit/polykit-x-monosynth

The Polykit X1 is a DIY semi-modular, analog, patchable synthesizer

Size: 8.42 MB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 58 - Forks: 3

LUMC/vtools

Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed

Language: Python - Size: 204 KB - Last synced: about 1 month ago - Pushed: 9 months ago - Stars: 1 - Forks: 1

mpieva/heffalump

Udo Stenzel’s Heffalump — a file format that stores genetic variation and the tool to work with it [MIRROR]

Language: Haskell - Size: 320 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

Zilong-Li/vcfppR

vcfpp.h + htslib + Rcpp == fast VCF/BCF

Language: C - Size: 9.19 MB - Last synced: 18 days ago - Pushed: 20 days ago - Stars: 8 - Forks: 1

jeroendesloovere/vcard

This vCard PHP library can easily parse or generate/export vCards as .vcf

Language: PHP - Size: 470 KB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 491 - Forks: 185

davetang/learning_vcf_file

Learning the Variant Call Format

Language: Perl - Size: 42.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 135 - Forks: 40

lpembleton/gatk4-when-did-dot-leave

Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./.

Size: 76.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

bihealth/vcfpy

Python 3 library with good support for both reading and writing VCF

Language: Python - Size: 1.25 MB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 83 - Forks: 17

Illumina/hap.py

Haplotype VCF comparison tools

Language: C++ - Size: 177 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 388 - Forks: 119

TimD1/vcfdist

vcfdist: Accurately benchmarking phased variant calls

Language: C++ - Size: 61.4 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 63 - Forks: 4

hail-is/hail

Cloud-native genomic dataframes and batch computing

Language: Python - Size: 118 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 925 - Forks: 235

mapaiva/vcard-go

A minimal library to manipulate vCard files using Golang

Language: Go - Size: 31.3 KB - Last synced: 11 days ago - Pushed: almost 2 years ago - Stars: 9 - Forks: 7

lvn3668/variantAnnotation

Variant annotation of vcf file using exac and vep

Language: Python - Size: 16.8 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

Moduland/csv2vcf

🔧 Simple script in python to convert CSV files to VCF

Language: Python - Size: 810 KB - Last synced: 15 days ago - Pushed: about 1 month ago - Stars: 70 - Forks: 23

collaborativebioinformatics/DSVifier

A bioinformatics pipeline for rapidly evaluating variants and identifying causal variants.

Language: C++ - Size: 9.71 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

IPK-BIT/divbrowse

A web application for interactive visualization and exploratory data analysis of variant call matrices

Language: Svelte - Size: 2.6 MB - Last synced: 9 days ago - Pushed: 10 months ago - Stars: 15 - Forks: 1

labsquare/cutevariant

A standalone and free application to explore genetics variations from VCF file

Language: Python - Size: 69.2 MB - Last synced: about 9 hours ago - Pushed: 1 day ago - Stars: 89 - Forks: 20

parkerpayne/vcf-search

Lightweight standalone tool to reduce size of VCF files through filtering

Language: Python - Size: 12.7 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

vembrane/vembrane

vembrane filters VCF records using python expressions

Language: Python - Size: 18.4 MB - Last synced: about 9 hours ago - Pushed: about 1 month ago - Stars: 56 - Forks: 5

chrovis/varity

Variant translation library for Clojure

Language: Clojure - Size: 843 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 6 - Forks: 2

chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

Language: Clojure - Size: 35.1 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 88 - Forks: 12

akcansoft/XLS-to-VCF

This Excel file exports contact information from a table to a vcf file

Language: VBA - Size: 54.7 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 7 - Forks: 3

wassermanlab/Variant_catalogue_pipeline

Variant catalogue pipeline

Language: HTML - Size: 5.78 MB - Last synced: 7 days ago - Pushed: 4 months ago - Stars: 22 - Forks: 7

umccr/vcf_stuff

📊Evaluating, filtering, comparing, and visualising VCF

Language: Jupyter Notebook - Size: 40.3 MB - Last synced: 8 days ago - Pushed: about 1 year ago - Stars: 26 - Forks: 3

zhanxw/seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

Language: C - Size: 6.99 MB - Last synced: 22 days ago - Pushed: 3 months ago - Stars: 30 - Forks: 12

TheSergeyPixel/Diablo_G25

Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.

Language: Python - Size: 15.4 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

x-lab/samplyzer

An R package and Web App for efficient quality control of human whole-genome and whole-exome datasets

Language: R - Size: 958 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

hudeany/dbexport

Java tool to export data ifrom database in files

Language: Java - Size: 57.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 3

SBence/vcfmerge 📦

Language: Python - Size: 5.86 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

varfish-org/varfish-dev-docs

VarFish software development documentation

Language: Makefile - Size: 34.2 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

brentp/peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Language: Jupyter Notebook - Size: 39.3 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 125 - Forks: 38

alexcoppe/genomicpp

A bunch of C++ programs for working with bioinformatics files

Language: C++ - Size: 32.2 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

bolorundurowb/vCardLib

A .NET standard library for reading vCard files

Language: C# - Size: 805 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 22 - Forks: 14

animesh-chouhan/vcf-creator

Generate vCard file from CSV

Language: Python - Size: 945 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 6 - Forks: 1

bejobioinformatics/tabixpy

Tabix reader written 100% in Python

Language: Python - Size: 51.1 MB - Last synced: 19 days ago - Pushed: over 2 years ago - Stars: 7 - Forks: 0

zarrine905/vcf_to_bed_intersect

Language: Python - Size: 31.3 KB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

mixerp/MixERP.Net.VCards

vCard Serializer and Parser for C#

Language: C# - Size: 294 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 69 - Forks: 41

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 143 - Forks: 28

jaredhowland/contacts

📇 PHP library for address book contacts (make .vcf vCards for contacts)

Language: PHP - Size: 1.64 MB - Last synced: 12 days ago - Pushed: 7 months ago - Stars: 4 - Forks: 1

varfish-org/hgvs-rs

A port of biocommons/hgvs to the Rust programming language

Language: Rust - Size: 1.07 MB - Last synced: 22 days ago - Pushed: 27 days ago - Stars: 8 - Forks: 2

valentinodileonardo/NumberGenerator

Bulk-Generation tool for international mobile phone numbers (Google CSV/VCF).

Language: C# - Size: 733 KB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

suaskot/vcf-to-csv-converter Fork of pstrinic/vcf-to-csv-converter

.vcf & .vcard to .csv (batch) converter

Language: Python - Size: 31.3 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

XuewenWangUGA/StrPhaser

The novel bioinformatics tool for building phased STR allelic sequences from VCF file

Size: 46.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0