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alstructure

An R package that implements the ALStructure algorithm for estimating the admixture model of genetic population structure

alstructure-manuscript

Data and code utilized in "A likelihood-free estimator of population structure bridging admixture models and principal components analysis", by Cabreros and Storey

barnone

Match barcodes in sequencing data based on Levenshtein distance

biobroom

Tidy up computational biology objects

bnpsd

R package to model and simulate admixed populations

dnamix

DNAMIX is a computer program to calcluate likelihood ratios as they pertain to mixed DNA samples encountered in forensic science.

edge

R package for identifying differentially expressed genes from genome-wide gene expression profiling studies.

eigenr2

factorial-ma-rs

Supplementary Materials for the manuscript "A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays" by Robinson, Wang, and Storey

ffdr

Functional FDR package

gcat

This package has been renamed gcatest: https://github.com/StoreyLab/gcatest

gcatest

genotype conditional association test

human-differentiation-manuscript

Details on the data analysis for "New kinship and F_ST estimates reveal higher levels of differentiation in the global human population" by Ochoa and Storey

lfa

logistic factor analysis

odp_general_studies

Reproducible analyses for "The optimal discovery procedure for significance analysis of general gene expression studies" by Bass and Storey

popkin

R package to estimate kinship and FST from SNP data

qvalue

R package to estimate q-values and false discovery rate quantities.

qvalue-shiny

a shiny website for the q-value package.

reading

A collection of papers and books that Storey Lab members should read and others may find useful

shwe-manuscript

sparta

Dividing RNA-Seq reads based on their ancestral genotype

storeylab.github.io

subseq

Subsampling of high-throughput sequencing count data

superseq

Assessing the increase in power from increasing read depth in a given RNA-Seq study

superseq-manuscript

terastructure

TeraStructure is a new algorithm to fit Bayesian models of genetic variation in human populations on tera-sample-sized data sets (10^12 observed genotypes, i.e., 1M individuals at 1M SNPs). This package provides a scalable, multi-threaded C++ implementation that can be run on a single computer.

trigger-devel