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ashr

An R package for adaptive shrinkage

automaticanalysis

Automatic analysis

awesome-network-analysis

A curated list of awesome network analysis resources.

bayesprism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

bigpca

development for CRAN package, 'bigpca' which provides pca and other functionality for the bigmemory suite of packages

blade

BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data

canlabcore

Core tools required for running Canlab Matlab toolboxes.

computing-communities-in-large-networks-using-random-walks

Implementation of a random-walk based algorithm Walktrap to efficiently find clusters in graphs.

cufflinks

data_availability_eradulescu

datasharing

The Leek group guide to data sharing

devmeth450k

Supplementary Code for "Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex"

dgca

Differential Gene Correlation Analysis

emagma-tutorial

A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.

epi2loc

Epistatic and penetrance models for two-locus genetic

epispot

epispot R package - Annotation-driven approach for large-scale joint regression with multiple responses

eugenia_test

fastconsensus

Fast consensus clustering in networks

fcma-toolbox

Princeton Full Correlation Matrix Analysis (FCMA) Toolbox

gephi

Gephi - The Open Graph Viz Platform

h2o-tutorials

Tutorials and training material for the H2O Machine Learning Platform

isoform_brainspan

kge_predictions_gd

Predicting Gene-Disease Associations

l3

Network-based prediction of protein interactions

latentcor

latentcor is an R package provides estimation for latent correlation with mixed data types (continuous, binary, truncated and ternary).

ldak-gbat-paper-scripts

ldsc

LD Score Regression (LDSC)

libsvm

limmade2

This package is deprecated - see RNAseqDE.

lindquist_dynamic_correlation

Martin Lindquist's dynamic correlation toolboxes. Designed for fMRI analysis, useful for other applications too.