jcgrenier's Stars
marbl/CHM13
The complete sequence of a human genome
vcflib/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
marbl/verkko
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
molgenis/systemsgenetics
Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
odelaneau/GLIMPSE
Low Coverage Calling of Genotypes
andersen-lab/ivar
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
connor-lab/ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
cytoscape/cytoscape-automation
Collection of scripts that include programmatic io and control of Cytoscape
vcflib/bio-vcf
Smart VCF parser DSL
pridiltal/stray
stray {Search and TRace AnomalY}. Full paper is available from https://arxiv.org/pdf/1908.04000.pdf :dog::dog::dog::dog::cat: :dog: :dog::dog::dog::dog:
KrishnaswamyLab/Multiscale_PHATE
Creating multi-resolution embeddings and clusters from high dimensional data
PoonLab/covizu
Rapid analysis and visualization of coronavirus genome variation
virus-evolution/gofasta
Joyvalley/GWAS_Flow
GPU accelerated GWAS framework based on TensorFlow
browning-lab/flare
The flare program performs local ancestry inference
mccoy-lab/MAGE
Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.
xiaolei-lab/SIMER
Data Simulation for Life Science and Breeding
yairf/SDS
R code to compute the Singleton Density Score (SDS)
artic-network/primer-schemes
Primer schemes for real-time genome epidemiology
vector-engineering/covidcg
A COVID-19 CoV Genetics (CG) browser to inform therapeutics development
broadinstitute/GATK-for-Microbes
cbg-ethz/cojac
mpieva/mapAD
An aDNA aware short-read mapper
slowkow/allelefrequencies
📂 HLA allele frequencies in tab-delimited format, downloaded from AFND.
fogellab/multiWGCNA
an R package for deep mining gene co-expression networks in multi-trait expression data
NicolaDM/phastSim
fast sequence evolution simulation for SARS-CoV-2 and similar
pephco/quickLD
quickLD, a large-scale, long-range Linkage Disequilibrium analysis tool utilizing parallel CPU, GPU or heterogeneous computing.
daifengwanglab/Varmole
rochefca/DIETNETWORK
Public code for Diet Network
billzt/pyOverChain
a python pipeline to generate chain files between different genome assemblies for LiftOver.