stephenslab Goto Github PK

ash

Code and analyses from "FDR: A New Deal" paper

ash-paper-docker

Docker image for adaptive shrinkage paper

ashlar

Workflow template

awesome-single-cell

List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

causal-twas

website for causal TWAS project

cicero

confounding-polygenic

For discussing work related to confounding vs polygenicity

cormotif

Correlation motif model.

count-clustering

Code and data reproducing results from our PLOS Genetics paper "Visualizing the structure of RNA-seq expression data using grade of membership models"

cv

R code for simple and fast k-fold cross-validation.

daarem

A few illustrations of the daarem method.

dashr

R package for Dirichlet adaptive shrinkage and smoothing

ddd

slides for DDD site visit

dsc

Repo for Dynamic Statistical Comparisons project

dsc-blm

DSC benchmark for Bayesian linear models.

dsc-finemap

DSC for comparing fine-mapping methods.

dsc-linreg

DSC for comparing accuracy of linear regression methods in prediction.

dsc-log-fold-change

dsc to compare approaches to estimating/testing log-fold-change from counts

dsc-normalmeans

repo for dynamic statistical comparison of normal means methods

dsc-reg-debug

dsc-regression

Application of DSC2 framework to a range of regression models.

dsc-smooth-gaussian

dynamic statistical comparison of nonparametric regression (smoothing) methods, data with gaussian errors

dsc-wiki

Documents / write-up introducing dynamic statistical comparison

dsc_susierss

Companion code repository for the paper, "Fine-mapping from summary data with the Sum of Single Effects model".

dscr-smash

Source code implementing Gaussian denoising simulations for Xing & Stephens (2016).

eb-linreg-dsc

ebayesthresh

R package for Empirical Bayes thresholding and related methods.

ebayesthresh2

Work on possible extensions to ebayesthresh—see stephenslab/ebayesthresh.

ebayesthresh_from_kan

R package for Empirical Bayes thresholding and related methods

ebhybrids

software for detecting hybrids, accounting for genotyping error and allelic dropout