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pharmacogenomics

Pharmacogenomics app for MedSavant

pnc_pathwayanalysis

Pathway analysis pipeline for PNC data (GWAS + GSEA)

poppathr

Population-based pathway analysis of SNP-SNP coevolution

powclui

POW! PDZ domain-peptide interaction prediction command line user interface

promoterpredictor

Using a SVM and 5 identified features, scan genomic coordinates for putative promoter regions

ratliver

a single-cell atlas of the rat liver

rcy3introworkshop

Introductory workshop for cytoscape automation with RCy3

retinasc

saber

Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.

saber-api-docs

API documentation for Saber

sc_variant_profiler

A variant calling pipeline for single-cell RNAseq data

scclustviz

Explore and share your scRNAseq clustering results

scrnaseqworkflow

Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz

singlelivercells

Scripts for processing single liver cells RNA-Seq 10X Genomics Data

sirenapp

socialnetworkapp

dropbox

studentprojectideas

Project ideas for summer and co-op students

summexpdr

Wrapper for SummarizedExperiment Objects for performing data integration + dimensionality reduction

tempora

Pathway-based trajectory inference method for time-series scRNAseq data

thematicmapapp

Thematic Map Cytoscape App

tor_ibin

towards-reliable-bioner

This repository contains the corpora and supplementary data, along with instructions for recreating the experiments, for our paper: "Towards reliable named entity recognition in the biomedical domain".

transfer-learning-bner-bioinformatics-2018

This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical named entity recognition with neural networks.

wordcloudplugin

WordCloud Cytoscape app