BaderLab/StudentProjectIdeas

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BaderLab/StudentProjectIdeas

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Project ideas for summer and co-op students

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.

CellAnnotationTutorial

Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods

Cytoscape_workflows

collection of notebooks with different cytoscape workflows

scClustViz

Explore and share your scRNAseq clustering results

Biomedical-Corpora

A collection of annotated biomedical corpora, which can be used for training supervised machine learning methods for various tasks in biomedical text-mining and information extraction.

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.

ecuda

STL-like containers (array, vector, matrix, cube) useable in device code.

EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.

HumanLiver

R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

Tempora

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

singleLiverCells

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

AgingMouseBrainCCInx

Predicted cell-cell interactions of the aging mouse brain

EPIC

This is the public repository for the EPIC tool.

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".

netDx

R package with netDx software and data for examples

scRNAseqWorkflow

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

MALAT1_threshold

GenomeClinic-PGX

Web application for clinical pharmacogenomic interpretation

CCInx

Build predicted cell-cell interaction networks from single-cell data.

cy3d-impl

3D Graph Renderer for Cytoscape using OpenGL

openPIP

The open protein interaction platform repo

MCODE

Cytoscape app that clusters a given network based on topology to find densely connected regions

SocialNetworkApp

AutoAnnotateApp

The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.

GeneEval

A Python library for evaluating gene embeddings.

MouseCortex

R data: Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling

EM-tutorials-docker

Jupyter Notebook

EnrichmentMap_docs

End-User Documentation for the EnrichmentMap Cytoscape App

Cell_Cycle_Theory

EnrichmentMap_monthlyGenesetBuild

EasycyRest

Suite of wrappers for CyREST functions in R

WordCloudPlugin

WordCloud Cytoscape app

Cytoscape-workshop-docker

Jupyter Notebook

pharmacogenomics

Pharmacogenomics app for MedSavant

biopax-jsonld

A BioPAX to/from JSON-LD format converter.

Web Ontology Language

covid19-dashboard

POPPATHR

Population-based pathway analysis of SNP-SNP coevolution

PNC_PathwayAnalysis

Pathway analysis pipeline for PNC data (GWAS + GSEA)

BreastCancer_PathwayAnalysis

BreastCancer Pathway Analysis performed for Nature/Nature Genetics paper 2017 (for ERNeg and Overall breast cancer)

RatLiver

a single-cell atlas of the rat liver

SummExpDR

Wrapper for SummarizedExperiment Objects for performing data integration + dimensionality reduction

gproxy

A proxy server for Google Analytics to bypass adblockers etc

Rcy3IntroWorkshop

Introductory workshop for cytoscape automation with RCy3

PromoterPredictor

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