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An open API service indexing awesome lists of open source software.
awesome-genetics-software
A list of cool software for genetic analysis and the like
https://github.com/snewhouse/awesome-genetics-software
- https://www.cog-genomics.org/plink/2.0/
- https://jmarchini.org/bgenie
- http://cnsgenomics.com/software/gcta/ - wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits
- https://github.com/bulik/ldsc
- https://github.com/choishingwan/PRSice - resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to linkage disequilibrium and P-value ("clumping"), and can be applied across multiple traits in a single run.
- https://github.com/tshmak/lassosum - wide meta-analyses, accounting for Linkage Disequilibrium (LD), via a reference panel. The reference panel is assumed to be in PLINK format. Summary statistics are expected to be loaded into memory as a data.frame/data.table.
- https://github.com/bvilhjal/ldpred - 9297(15)00365-1]
- https://github.com/gabraham/flashpca - price/software/) and shellfish (https://github.com/dandavison/shellfish). FlashPCA is based on the https://github.com/yixuan/spectra/ library.
- https://www.genetics.ucla.edu/software/admixture/
- https://github.com/DReichLab/EIG - 9 (EIGENSTRAT stratification correction)