quattro
Computational & Statistical Genetics. Associate Professor of Biostatistics at USC.
@mancusolab Los Angeles
Pinned Repositories
FactorGo
Software to infer latent pleiotropic components from GWAS summary data
ma-focus
MA-FOCUS: Multi-Ancestry Fine-mapping Of CaUsal gene Sets
sushie
Software to perform multi-ancestry SNP fine-mapping on molecular data
susiepca
Scalable Ultra-Sparse Bayesian PCA
traceax
Stochastic trace estimation using JAX
twas_sim
Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.
ASHG18
Notes
CLAPmagrittrCLAP
Improve the readability of R code with the pipe
DS2VCF
Annotate VCF file with dosages estimated from genotype likelihoods
mister
Simulation study of various Mendelian Randomization approaches using summary data
quattro's Repositories
quattro/CLAPmagrittrCLAP
Improve the readability of R code with the pipe
quattro/mister
Simulation study of various Mendelian Randomization approaches using summary data
quattro/ASHG18
Notes
quattro/DS2VCF
Annotate VCF file with dosages estimated from genotype likelihoods
quattro/labtools
Repo for common tools/scripts
quattro/optfun
approximate optimization in demented times
quattro/PAINTOR_V3.0
Fast, integrative fine mapping with functional data
quattro/BFFs
comparison of a few ways to infer posterior values under a causal linear mixed model
quattro/egrm
quattro/flashpca
Fast Principal Component Analysis of Large-Scale Genome-Wide Data
quattro/fusion_twas
methods for functional summary-based imputation
quattro/geno-sugar
Utilities for handling genetic data for GWAS
quattro/geosnp
quattro/humgen_hw
quattro/jax
Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
quattro/limix-feedstock
A conda-smithy repository for limix.
quattro/linear-dag
quattro/LinearThunderdome
Thunderdome of linear models in ill-conditioned settings
quattro/lineax
Linear solvers in JAX and Equinox. https://docs.kidger.site/lineax
quattro/numpyro
Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.
quattro/optimistix
Nonlinear optimisation (root-finding, least squares, ...) in JAX+Equinox. https://docs.kidger.site/optimistix/
quattro/prior_var_empbayes
Testing empirical bayes for inference of prior variance terms in finemapping
quattro/pyfizi-feedstock
A conda-smithy repository for pyfizi.
quattro/Randomly-Pivoted-Cholesky
Code for the paper "Randomly pivoted Cholesky: Practical approximation of a kernel matrix with few entry evaluations"
quattro/REMLSketch
Sketching version of REML inference
quattro/sleuth
Differential analysis of RNA-Seq
quattro/SnpSift
quattro/spa
a tool for analysis of spatial structure in genetics data
quattro/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
quattro/TWAS_HUB