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advdatasci

aifi-swanson-teaseq

Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization

ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

annotables

R data package for annotating/converting Gene IDs

assocplots

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

bash-oneliner

A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.

bhr

Suite of heritability and genetic correlation estimation tools for exome-sequencing data

biccn_m1_evo

Analysis for BICCN cross-species primary motor cortex project

biotools

A list of useful bioinformatics resources

bnmf-clustering

boxplotr.shiny

shiny application to generate box plots with R

ccmdr

Clinical Connectivity Mapping for Drug Repositioning

datasharing

The Leek group guide to data sharing

deepcpg

Deep neural networks for predicting CpG methylation

deepwas

DeepWAS: Directly integrating regulatory information into GWAS using machine learning

dmrff

dnamethyage

Predict epigenetic age from DNA methylation data

dplyr

dplyr: A grammar of data manipulation

drugsets

Drug gene set analysis (DRUGSETS) is a command line interface (CLI) tool implemented in python to perform genetically informed drug repositioning using drug gene set analysis in MAGMA.

epidish

This package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.

episcore

Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles

focus

FOCUS: Fine-mapping Of CaUsal gene Sets

fuma_scrna_data

Descriptions/scripts for pre-process and processed data for FUMA cell specificity analyses (scRNA-seq)

fusion_twas

methods for functional summary-based imputation

gaworkshop

Genome Analysis Workshop (Jena 2016) material

genetic_support

Refining the impact of genetic evidence on clinical success

genomicsem

R-package for structural equation modeling based on GWAS summary data

ggman

R package to create manhattan plots using ggplot

grep

GREP: Genome for REPositioning drugs