intermine : A powerful open source data warehouse system
author: intermine
created: 2012-07-02 10:25:18
api bioinformatics biology clojure clojurescript data-visualisation data-visualization data-warehouse genetics genomics java lgplv3 open-source opensource perl postgresql python tomcat tomcat8 webservices


rvtests : Rare variant test software for next generation sequencing data
author: zhanxw
created: 2013-01-09 20:58:39
association-analysis c-plus-plus genetics genotype gwas kernel meta-analysis next-generation-sequencing ngs rare-variant skat umich variants vcf-files c++


seq_view : Vim-like program for viewing genetic sequences on the command line (ncurses).
author: brendane
created: 2013-01-29 16:30:29
bioinformatics c-plus-plus cli command-line curses fasta fastq genetics sequences text-based unix visualization c++


TriFusion : Streamlining phylogenomic data gathering, processing and visualization
author: ODiogoSilva
created: 2014-02-11 17:13:31
genetics gui kivy orthologues phylogenetics phylogenomic python visualization


GeneticThesaurus : Thesaurus for genetic variants
author: tkonopka
created: 2014-05-02 14:31:04
genetic-variants genetics genomic-regions repetitive-regions thesaurus variant-calling java


SmallTools : Small tools for genetics research
author: UMCUGenetics
created: 2014-08-22 16:08:57
genetics python tools


jtopham_dev : R, python, perl, RMD and makefile scripts for various bioinformatics projects
author: jtopham
created: 2014-09-19 19:22:26
bioinformatics computational-biology epigenetics genetics html


BayesTwin : Developmental version of R package BayesTwin
author: ingaschwabe
created: 2014-11-09 18:01:52
bayesian genetics heritability item-response-theory mcmc-sampler package psychometrics r


pyplink : Python module to read binary Plink files.
author: lemieuxl
created: 2014-12-02 14:34:17
bioinformatics genetics genomics python


pyGenClean : Automated genetic data clean up procedure in Python.
author: lemieuxl
created: 2014-12-02 21:09:22
bioinformatics genetics genomics python


atelier-prediction-genomique : Atelier de prédiction et sélection génomique.
author: timflutre
created: 2015-01-26 17:48:23
enseignement genetics genetique inra teaching html


genipe : Genome-wide imputation pipeline
author: pgxcentre
created: 2015-02-09 18:44:51
bioinformatics genetics genomics python


Structure_threader : A wrapper program to parallelize and automate runs of "Structure", "fastStructure" and "MavericK".
author: StuntsPT
created: 2015-03-03 12:56:42
clustering doi genetics parallelize pypi python science structure structure-threader wrapper


KEGG-Crawler : A parallel web crawler for the retrieval of KEGG metabolic and genomics data.
author: mentatpsi
created: 2015-03-06 23:33:31
genetics kegg kegg-reaction keggrest metabolites pathway python reactions


BGData : A Suite of Packages for Analysis of Big Genomic Data
author: QuantGen
created: 2015-03-16 21:33:22
genetics genomics gwas r r-pkg


epistasis : A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
author: harmslab
created: 2015-04-01 22:46:44
epistasis evolution genetics genotype-phenotype-maps high-order modeling nonlinear python


notebooks-nonlinear-high-order-epistasis : Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"
author: harmslab
created: 2015-04-20 16:14:10
epistasis genetics genotype-phenotype-maps high-order-epistasis jupyter-notebooks statistics jupyter notebook


BEDMatrix : A matrix-like wrapper around PLINK .bed files
author: QuantGen
created: 2015-05-21 19:29:11
bed cran genetics genomics ped plink r r-pkg


stackr : stackr: an R package to run stacks software pipeline
author: thierrygosselin
created: 2015-05-23 03:21:36
filter gbs genetics genomic-data-analysis genomics genomics-visualization genotype-likelihoods genotyping-by-sequencing rad radseq radseq-data stackr r


coRge : Evaluation of Simultaneous Inference Methods for the Human Genome.
author: Chris1221
created: 2015-06-11 17:35:33
genetics high-performance-computing multiple-testing-correction simulation r


pedRSP : Pedigree Relatedness Summary Parameters R package
author: jraffa
created: 2015-07-08 23:26:51
eigenvalues genetics heritability pedigree power reproducible-research r


gpmap : A Python API for managing genotype-phenotype map data
author: harmslab
created: 2015-07-24 20:21:38
evolution genetics genotype-phenotype-maps networkx python


region-plot : A tool to plot significant regions of GWAS
author: pgxcentre
created: 2015-08-17 17:42:50
bioinformatics genetics genomics plot python


impute : Automated imputation pipeline for arbitrary dataset and reference panels.
author: Chris1221
created: 2015-08-18 17:12:16
genetics imputation snps shell


intermediate : small R utility for mediation analysis
author: simecek
created: 2015-09-24 22:46:11
genetics mediation-analysis package r


rss : Regression with Summary Statistics.
author: stephenslab
created: 2015-09-28 22:49:45
bayesian-methods genetics genomics gwas regression summary-statistics matlab


HiGWAS : Lasso method for the estimation of joint genetic effects in GWAS
author: wzhy2000
created: 2015-10-11 20:07:33
genetics gwas joint-effect lasso package r c++


hase : Framework for efficient high-dimensional association analyses.
author: roshchupkin
created: 2015-10-14 10:37:55
genetics gwas omics python-packages python


bcfanno : A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file
author: shiquan
created: 2015-10-20 06:01:00
annotations bcf genetics interpretation variants vcf c


hail : Scalable genomic data analysis.
author: hail-is
created: 2015-10-27 20:55:42
bioinformatics genetics genomics gwas python scala spark vcf


symDMatrix : Partitioned Symmetric Matrices
author: QuantGen
created: 2015-11-03 20:58:08
genetics genomics r r-pkg


inbix : In silico research group's bioinformatics toolbox for network and machine learning analysis
author: hexhead
created: 2015-11-04 15:10:13
analyses bioinformatics genes genetics interactions microarray networks plink relief-f rna-seq snps systems-biology c++


GWA_tutorial : A comprehensive tutorial about GWAS and PRS
author: MareesAT
created: 2015-11-27 17:43:12
genetics gwas plink population-structure prs qc r unix


genetic-mapper : SVG Genetic Map Drawer
author: pseudogene
created: 2015-12-07 15:02:44
bioinformatics genetic-maps genetics perl-script svg perl


docker-stacks : Stacks is a software pipeline for building loci from short-read sequences - Now in a Docker
author: pseudogene
created: 2015-12-14 13:38:11
bioinformatics docker-image docker-stacks genetics rad sequencing shell


wormbase : Caenorhabditis elegans genome annotations from WormBase.
author: steinbaugh
created: 2015-12-17 23:04:52
celegans genetics genome-annotations metadata r


GeneaPy : A collection of scripts to help aid PCR-based genetic variant validations.
author: superDross
created: 2016-01-07 21:00:25
genetics next-generation-sequencing pcr pyensembl python sanger


GeneDoc : A Full Featured Multiple Sequence Alignment Editor.
author: karlnicholas
created: 2016-01-20 02:04:11
genetic-algorithms genetic-programming genetics visualcplusplus visualcpp c++


manhattan_generator : Manhattan plot Generator
author: pgxcentre
created: 2016-02-08 18:40:53
bioinformatics genetics genomics plot python


VerifyBamID : A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
author: Griffan
created: 2016-02-15 14:47:35
bam bioinformatics biostatistics contamination cram dna-sequences genetics qc-analysis mupad


locuszoom-standalone : Create regional association plots from GWAS or meta-analysis
author: statgen
created: 2016-03-02 21:51:44
bioinformatics genetics visualization python


fGWAS : GWAS tools for longitudinal genetic traits based on fGWAS statistical model
author: wzhy2000
created: 2016-03-07 03:15:36
fgwas genetics gwas longitudinal r


xpclr : Code to compute the XP-CLR statistic to infer natural selection
author: hardingnj
created: 2016-03-23 14:55:55
bioinformatics genetics popgen selection python


23andme-tools : Convert 23andMe data to VCFs
author: genepi
created: 2016-05-06 20:21:37
fileformat genetics imputation vcfs java


genetic-surrogates : Data, code, and results for a research paper investigating surrogates for genetic data in conservation planning
author: jeffreyhanson
created: 2016-05-12 01:23:22
aflp biodiversity conservation genetics plants reproducible-paper reproducible-research science tex


phenopolis : An Open Platform for Harmonisation & Analysis of Sequencing & Phenotype Data
author: phenopolis
created: 2016-06-11 15:41:27
database genetics phenotype server javascript


CRESTseq : CREST-seq peak calling.
author: r3fang
created: 2016-06-16 02:22:04
bioinformatics crispr enhancer gene-regulation genetics samtools c++


R : R packages for genetic and clustered/longitudinal data
author: jinghuazhao
created: 2016-06-17 06:11:36
genetics imputation lmm fortran


DOMINO : Development of molecular markers in non-model organisms
author: molevol-ub
created: 2016-07-04 14:39:47
bioinformatics-pipeline domino evolution genetics graphical-user-interface molecular-markers perl user-friendly


ksburden : A test for distributional differences between cases and controls
author: rmporsch
created: 2016-07-07 07:10:06
genetics simulation statistics test c++


model-free-data : Case-control genetics datasets evolved to be epistatic
author: greenelab
created: 2016-07-18 13:48:17
biodata-mining dataset epistasis genetics moore-lab open-data simulation snps postscript


SexSpecificGraph : R functions for the sex-specific graph analysis
author: PhilBertrand
created: 2016-07-26 08:23:15
genetics landscape-data sensitivity-analysis sex-specific-graphs topology r


mprsq : Massively Parallel RNA-seq Project
author: WormLabCaltech
created: 2016-08-15 22:54:16
bioinformatics genetics rna-seq transcriptome jupyter notebook


Neanderthal : The companion website of the Neanderthal’s Synapse project.
author: GHFC
created: 2016-08-23 08:00:16
brain companion-website denisovan genetics human-lineage neanderthal pasteur population-genetics primates synapse javascript


mri_transcriptomics : Gene set enrichment analysis of the transcriptomic associations of the T1-w/T2-w MRI.
author: jritch
created: 2016-09-18 18:39:51
computational-neuroscience genetics imaging python r


OSGenome : An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies
author: mentatpsi
created: 2016-10-30 01:46:57
23andme data-crawling flask genetic-data genetics genome kendo python raw-data snpedia snps


pRs : Toolkit for the efficient construction and analysis of polygenic risk scores in R.
author: Chris1221
created: 2016-11-03 11:53:06
genetics plink polygenic-risk-scores r


GslCore : Core library and basic plug-ins for the Amyris Genotype Specification Language (GSL) compiler.
author: Amyris
created: 2016-11-22 09:32:57
bioinformatics biology compiler genetics genotype-specification-language gsl synthetic-biology f#


pgltools : Paired Genomic Loci Tool Suite
author: billgreenwald
created: 2016-12-14 17:35:42
chia-pet chromosome contacts genetics genomics hi-c loci locus paired-loci pgl pgl-files python


Synopsys-Project-2017 : A deep learning based bioinformatics project on epigenetics in Type 2 Diabetes.
author: minhoolee
created: 2016-12-20 19:32:15
bioinformatics deep-learning diabetes genetics keras synopsys jupyter notebook


Sequence-database-curator : This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
author: Eslam-Samir-Ragab
created: 2017-01-12 23:44:45
bioinformatics curator database fasta fastq gene genetics genomics metagenomics ncbi nucleotide protein proteomics redundancy sequence python


WikiGenomesBase : A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.
author: SuLab
created: 2017-01-18 21:24:37
annotation-tool bioinformatics database genetics genomics molecular-biology proteomics research website wikidata html


MendelianSwift : A protocol-oriented framework for solving bioinformatics problems
author: cbrenneisen
created: 2017-01-22 21:02:46
bioinformatics framework genetic-algorithm genetics informatics protocol-oriented-framework swift swift4-2


adam-playground : Collection of some function to deal with ADAM
author: antonkulaga
created: 2017-01-26 12:33:19
adam bionformatics genetics genomics scala spark


Mouse_Study_Pipeline : (Archived) This page is a record of my first formal NGS Project for Dr. Matesic of University of South Carolina (USC).
author: Volcanix280
created: 2017-02-02 02:32:13
bioinformatics-pipeline bioinformatics-scripts fastq genetics ngs ngstools pbs sra sra-files tophat


LEGIT : An R package for the Latent Environmental & Genetic InTeraction (LEGIT) model
author: AlexiaJM
created: 2017-02-13 15:42:43
environment genetic-variants genetics glm gxe gxe-modelling interactions latent-variable-models latent-variables r


LEGIT_SAS : SAS macros for the Latent Environmental & Genetic InTeraction (LEGIT) model
author: AlexiaJM
created: 2017-02-13 16:33:36
environment genetics glm gxe interactions latent-variable-models macros sas


genexp : Gene predictor and coding potential calculator, largely a WIP, learning experience
author: wenkesj
created: 2017-02-16 04:43:24
bioinformatics genetics go


DDDNonCoding2017 : Code for paper published in March, 2017 analysing the role of de novo mutations in severe developmental disorders (part of the deciphering developmental disorders project).
author: pjshort
created: 2017-02-18 12:44:24
genetics r


RADtyping : RADtyping: a user-defined perl procedure for performing de novo RAD genotyping in mapping populations.
author: jinzhuangdou
created: 2017-02-24 09:33:23
bioinformatics-pipeline genetics snp perl


easyGEN : A suite of packages for quantiative genetics analysis and more!
author: camult
created: 2017-02-25 06:02:23
blupf90 dmu genetics r


gggenes : ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
author: wilkox
created: 2017-03-02 07:16:19
genetics ggplot2 r


bltools : Unix-style text manipulation tools for biological sequence data.
author: brendane
created: 2017-03-05 17:07:12
bioinformatics biological-sequences c-plus-plus-14 command-line fasta fastq genetics grep head seqan sequences tail unix unix-philosophy unix-style c++


python-mendel : This is a simple python implementation of Gregor Mendel's heredity rule
author: Splinter0
created: 2017-03-05 19:30:46
genetics python science


rna-recursion : A Java program that checks RNA similarity between strings.
author: otakar-sst
created: 2017-03-06 18:17:47
codeclimate csa genetics java protein-structure recursion rna rna-seq sst


BAD_days : Bioinformatics Awareness Days
author: trallard
created: 2017-03-09 10:24:21
bioinformatics genetics jupyter-notebook r rna-seq jupyter notebook


PPI_network_pipeline : Pipeline to create and analyze protein-protein interaction networks.
author: lelimat
created: 2017-03-10 20:08:00
genetics network-analysis networkx ppi protein-protein-interaction python


solving-tsp-with-genetic-algorithms : Travelling Salesperson Problem solved using various genetic algorithms
author: niemtec
created: 2017-03-11 13:54:57
algorithms genetics heuristics java


geneparse : Clean interface to parse genotype files
author: pgxcentre
created: 2017-03-17 19:04:21
bioinformatics genetics genomics python


wISAM :
author: rcorty
created: 2017-03-22 20:12:17
genetics gwas gwas-tools lmm mixed-models html


pdVCF : Allows one to manipulate a VCF as a MultiIndex Pandas DataFrame
author: superDross
created: 2017-03-22 20:51:59
genetics pandas python3 vcf vcftools python


VcfFilterPy : VCF filtering tool
author: superDross
created: 2017-04-14 14:21:52
genetics python vcf vcf-filtering


molgenis-app-genetics : Repository containing modules and features for interacting with, searching through, and visualising genetic data
author: molgenis
created: 2017-04-20 10:25:27
genetics java javascript lifescience maven molgenis


genetic-tools : Утилиты для обработки данных генетических тестов
author: dionys
created: 2017-04-24 07:01:52
genetics isogg myheritage perl


Connect-to-Sequencing.com : Earn royalties and provide value to your users by allowing your users to store their genetic data at Sequencing.com.
author: SequencingDOTcom
created: 2017-04-25 18:33:27
dna gene genetic genetic-data genetics genome genomics sequencing python


codebits : snippets of code useful in bioinformatics
author: AidanQuinn
created: 2017-04-25 22:40:18