Sylvanus Toikumo's Projects
Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization
Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc
R data package for annotating/converting Gene IDs
A list of interesting genome browser or genome-browser-like implementations
A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.
Suite of heritability and genetic correlation estimation tools for exome-sequencing data
Analysis for BICCN cross-species primary motor cortex project
A list of useful bioinformatics resources
shiny application to generate box plots with R
Clinical Connectivity Mapping for Drug Repositioning
The Leek group guide to data sharing
Deep neural networks for predicting CpG methylation
DeepWAS: Directly integrating regulatory information into GWAS using machine learning
Predict epigenetic age from DNA methylation data
dplyr: A grammar of data manipulation
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.
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.
Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
FOCUS: Fine-mapping Of CaUsal gene Sets
Descriptions/scripts for pre-process and processed data for FUMA cell specificity analyses (scRNA-seq)
methods for functional summary-based imputation
Genome Analysis Workshop (Jena 2016) material
Refining the impact of genetic evidence on clinical success
R-package for structural equation modeling based on GWAS summary data
R package to create manhattan plots using ggplot
GREP: Genome for REPositioning drugs