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ashg18

Notes

bffs

comparison of a few ways to infer posterior values under a causal linear mixed model

clapmagrittrclap

Improve the readability of R code with the pipe

ds2vcf

Annotate VCF file with dosages estimated from genotype likelihoods

egrm

flashpca

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

fusion_twas

methods for functional summary-based imputation

geno-sugar

Utilities for handling genetic data for GWAS

geosnp

gsustatml

GSU Statistical ML Reading Group

humgen_hw

jax

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

kgem

KGEM: Scala implementation of Reconstruction of viral population algorithm for single-amplicon sequencing data

labtools

Repo for common tools/scripts

limix-feedstock

A conda-smithy repository for limix.

linear-dag

linearthunderdome

Thunderdome of linear models in ill-conditioned settings

lineax

Linear solvers in JAX and Equinox. https://docs.kidger.site/lineax

mister

Simulation study of various Mendelian Randomization approaches using summary data

networkx

Official NetworkX source code repository.

numpyro

Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.

optfun

approximate optimization in demented times

optimistix

Nonlinear optimisation (root-finding, least squares, ...) in JAX+Equinox. https://docs.kidger.site/optimistix/

paintor_v3.0

Fast, integrative fine mapping with functional data

prior_var_empbayes

Testing empirical bayes for inference of prior variance terms in finemapping

pyfizi-feedstock

A conda-smithy repository for pyfizi.

randomly-pivoted-cholesky

Code for the paper "Randomly pivoted Cholesky: Practical approximation of a kernel matrix with few entry evaluations"

remlsketch

Sketching version of REML inference

sleuth

Differential analysis of RNA-Seq

snpsift