graphsim — Peer-reviewed • Rank 14.3 • Science 98%

graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)

Python Implementation of Codon Adaptation Index — Peer-reviewed • Rank 10.3 • Science 93%

Python Implementation of Codon Adaptation Index - Published in JOSS (2018)

Syn-CpG-Spacer — Peer-reviewed • Rank 1.1 • Science 98%

Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral genomes with CpG dinucleotides - Published in JOSS (2024)

Genotify — Peer-reviewed • Rank 4.9 • Science 93%

Genotify: Fast, lightweight gene lookup and summarization - Published in JOSS (2018)

wolfexplorer — Peer-reviewed • Rank 4.4 • Science 93%

wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets - Published in JOSS (2018)

https://github.com/theislab/cellrank • Rank 16.8 • Science 67%

CellRank: dynamics from multi-view single-cell data

gene-normalizer • Rank 13.5 • Science 64%

Services and guidelines for normalizing genes

msprime • Rank 19.3 • Science 54%

Simulate genealogical trees and genomic sequence data using population genetic models

hail • Rank 24.2 • Science 46%

Cloud-native genomic dataframes and batch computing

cutevariant • Rank 12.0 • Science 54%

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

umx • Rank 14.0 • Science 49%

Making Structural Equation Modeling (SEM) in R quick & powerful

kgp • Rank 8.6 • Science 54%

1000 Genomes Project Metadata R Package

https://github.com/broadinstitute/pyro-cov • Rank 6.6 • Science 54%

Pyro models of SARS-CoV-2 variants

https://github.com/ctriermaansson/dnafusion • Rank 11.1 • Science 49%

Identification of gene-fusions, including EML4-ALK

planet • Rank 12.6 • Science 46%

For inferring ancestry, gestational age, cell type proportions, and preeclampsia status from placental DNA methylation array data

https://github.com/biojulia/popgen.jl • Rank 7.1 • Science 49%

Population Genetics in Julia

gap • Rank 16.9 • Science 36%

R packages

BGData • Rank 11.1 • Science 39%

A Suite of Packages for Analysis of Big Genomic Data

rCNV • Rank 8.6 • Science 39%

An R package for detecting copy number variants from SNPs data

BiocHail • Rank 11.6 • Science 36%

Using hail via Basilisk

fwdpy11 • Rank 11.5 • Science 36%

Forward-time simulation in Python using fwdpp

biascorrector • Rank 11.4 • Science 36%

R package providing a shiny GUI to the functions implemented in rBiasCorrection

https://github.com/broadinstitute/funpipe • Rank 8.5 • Science 36%

A python3 library for building best practice fungal genomic analysis pipeline

epistasis • Rank 9.3 • Science 33%

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

https://github.com/cdcgov/tostadas • Rank 5.2 • Science 36%

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

lineage • Rank 14.5 • Science 26%

tools for genetic genealogy and the analysis of consumer DNA test results

statgenGWAS • Rank 13.7 • Science 26%

See https://biometris.github.io/statgenGWAS for a full description

statgenGxE • Rank 13.7 • Science 26%

See https://biometris.github.io/statgenGxE for a full description

https://github.com/biometris/statgensta • Rank 13.2 • Science 26%

See https://biometris.github.io/statgenSTA for a full description

https://github.com/biometris/statgenhtp • Rank 13.0 • Science 26%

See https://biometris.github.io/statgenHTP for a full description

BEDMatrix • Rank 10.7 • Science 26%

A matrix-like wrapper around PLINK .bed files

RIVER • Rank 12.9 • Science 23%

R package for RIVER (RNA-Informed Variant Effect on Regulation)

pygenclean • Rank 5.1 • Science 26%

Automated genetic data clean up procedure in Python.

cmappy • Rank 15.6 • Science 10%

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

FamAgg • Rank 14.4 • Science 10%

This is the development version of the FamAgg Bioconductor package.

genipe • Rank 9.8 • Science 13%

Genome-wide imputation pipeline

sRACIPE • Rank 10.3 • Science 10%

sRACIPE for bioconductor

gpmap • Rank 9.8 • Science 10%

A Python API for managing genotype-phenotype map data

https://github.com/biometris/statgenqtlxt • Science 26%

See https://biometris.github.io/statgenQTLxT for a full description

https://github.com/databio/bedms • Science 26%

Tool for standardization of genomics/epigenomics metadata

kalis • Science 39%

kalis: High Performance Li & Stephens Local Ancestry Inference

https://github.com/biometris/statgenmpp • Science 36%

See https://biometris.github.io/statgenMPP for a full description

germinate-vue • Science 75%

Germinate is an open source plant database infrastructure and application programming platform on which complex data from genetic resource collections can be stored, queried and visualized.

sme • Science 49%

A fast and scalable method to detect epistasis in complex traits from biobank-scale studies

maizesnp • Science 67%

SNP analysis of different maize (Zea mays L.) inbred lines in comparison to B73 as a reference line

https://github.com/cjabradshaw/demo-genetic • Science 49%

Code for SLiM 4.0 demo-genetic models examining the population effects of genetic rescue

recimap • Science 44%

Recimap (a reciprocal mapping tool) was developed as a bioinformatics command-line tool/pipeline to find rearrangements breakpoints between two closely related genomes.

https://github.com/biometris/statgenibd • Science 36%

See https://biometris.github.io/statgenIBD for a full description

theagingproteome • Science 18%

Source for a paper "The Aging Proteome: Is Aging Programmed in our Genes?"

parentageanalysisoh.net • Science 44%

A library for parentage analysis using efficiently computed opposing homozygote counts.

geneviewer • Science 26%

An R package designed for drawing gene arrow maps

snip • Science 44%

A utility package handling Single Nucleotide polymorphism data in Python

https://github.com/broadinstitute/repeatvariantsinccle • Science 26%

This repo is about the analysis if repeat variants in CCLE for the paper: "Werner Helicase Prevents Cell Death in Cancers with Microsatellite Instability by Resolving Large-scale Expanded (TA)n Repeats" of Wietmarschen et. al.

qtl-mapping • Science 26%

https://github.com/cjgeyer/sped • Science 23%

Multigene Descent Probabilities R Package

vencode • Science 13%

bumblebee • Science 13%

Quantify Disease Transmission Within and Between Population Groups

digital-brain • Science 18%

My eventual digital home.

eggla • Science 49%

Early Growth Genetics Longitudinal Analysis.

https://github.com/babinyurii/recan_gui • Science 36%

A web tool for recombination events analysis in viral genomes. Django based version of recan

gazoduc-nf • Science 44%

Nextflow Pipelines