Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by BaderLab
A curated list of projects in awesome lists by BaderLab .
https://github.com/baderlab/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.
bioinformatics biomedical-named-entity-recognition biomedical-text-mining deep-learning information-extraction machine-learning spacy
Last synced: 14 Oct 2024
https://github.com/baderlab/cellannotationtutorial
Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
Last synced: 05 Nov 2024
https://github.com/baderlab/scclustviz
Explore and share your scRNAseq clustering results
clustering-evaluation differential-expression r scrna-seq scrna-seq-analysis scrnaseq shiny single-cell ui
Last synced: 05 Nov 2024
https://github.com/baderlab/cytoscape_workflows
collection of notebooks with different cytoscape workflows
Last synced: 05 Nov 2024
https://github.com/baderlab/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.
Last synced: 05 Nov 2024
https://github.com/baderlab/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.
Last synced: 05 Nov 2024
https://github.com/baderlab/ecuda
STL-like containers (array, vector, matrix, cube) useable in device code.
Last synced: 05 Nov 2024
https://github.com/baderlab/enrichmentmapapp
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
Last synced: 05 Nov 2024
https://github.com/baderlab/humanliver
R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
dataset immunology liver r single-cell
Last synced: 05 Nov 2024
https://github.com/baderlab/tempora
Pathway-based trajectory inference method for time-series scRNAseq data
Last synced: 05 Nov 2024
https://github.com/baderlab/singlelivercells
Scripts for processing single liver cells RNA-Seq 10X Genomics Data
Last synced: 05 Nov 2024
https://github.com/baderlab/agingmousebrainccinx
Predicted cell-cell interactions of the aging mouse brain
Last synced: 05 Nov 2024
https://github.com/baderlab/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".
Last synced: 05 Nov 2024
https://github.com/baderlab/epic
This is the public repository for the EPIC tool.
Last synced: 05 Nov 2024
https://github.com/baderlab/netdx
R package with netDx software and data for examples
Last synced: 05 Nov 2024
https://github.com/baderlab/scrnaseqworkflow
Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz
Last synced: 05 Nov 2024
https://github.com/baderlab/ccinx
Build predicted cell-cell interaction networks from single-cell data.
Last synced: 05 Nov 2024
https://github.com/baderlab/genomeclinic-pgx
Web application for clinical pharmacogenomic interpretation
Last synced: 05 Nov 2024
https://github.com/baderlab/cy3d-impl
3D Graph Renderer for Cytoscape using OpenGL
3d-renderer cytoscape java jogl opengl
Last synced: 05 Nov 2024
https://github.com/baderlab/mcode
Cytoscape app that clusters a given network based on topology to find densely connected regions
Last synced: 05 Nov 2024
https://github.com/baderlab/openpip
The open protein interaction platform repo
Last synced: 05 Nov 2024
https://github.com/baderlab/autoannotateapp
The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.
Last synced: 05 Nov 2024
https://github.com/baderlab/geneeval
A Python library for evaluating gene embeddings.
Last synced: 05 Nov 2024
https://github.com/baderlab/mousecortex
R data: Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling
dataset neuroscience r single-cell
Last synced: 05 Nov 2024
https://github.com/baderlab/enrichmentmap_docs
End-User Documentation for the EnrichmentMap Cytoscape App
Last synced: 05 Nov 2024
https://github.com/baderlab/easycyrest
Suite of wrappers for CyREST functions in R
Last synced: 05 Nov 2024
https://github.com/baderlab/pharmacogenomics
Pharmacogenomics app for MedSavant
Last synced: 05 Nov 2024
https://github.com/baderlab/breastcancer_pathwayanalysis
BreastCancer Pathway Analysis performed for Nature/Nature Genetics paper 2017 (for ERNeg and Overall breast cancer)
Last synced: 05 Nov 2024
https://github.com/baderlab/rcy3introworkshop
Introductory workshop for cytoscape automation with RCy3
Last synced: 05 Nov 2024
https://github.com/baderlab/pnc_pathwayanalysis
Pathway analysis pipeline for PNC data (GWAS + GSEA)
Last synced: 05 Nov 2024
https://github.com/baderlab/poppathr
Population-based pathway analysis of SNP-SNP coevolution
coevoluton enrichment pathway-analysis population-genetics positive-selection
Last synced: 05 Nov 2024
https://github.com/baderlab/gproxy
A proxy server for Google Analytics to bypass adblockers etc
Last synced: 05 Nov 2024
https://github.com/baderlab/studentprojectideas
Project ideas for summer and co-op students
Last synced: 05 Nov 2024
https://github.com/baderlab/goslimmerapp
Gene Ontology Slimmer Cyotscape App
Last synced: 05 Nov 2024
https://github.com/baderlab/magic
Genomics browser for the Medulloblastoma Advanced Genomics International Consortium (MAGIC) project
Last synced: 05 Nov 2024
https://github.com/baderlab/mcode_docs
End-User Documentation for the MCODE Cytoscape App
Last synced: 05 Nov 2024
https://github.com/baderlab/networkslideshow
An app allowing for edges in a Cytoscape.js network to appear, disappear, and change with different frames.
Last synced: 05 Nov 2024
https://github.com/baderlab/expression-correlation
Cytoscape 3 app that computes a similarity network from either the genes or conditions in an expression matrix.
Last synced: 05 Nov 2024
https://github.com/baderlab/logrank.test_power
R function and document for power analysis of the log-rank test in survival analysis
Last synced: 05 Nov 2024
https://github.com/baderlab/docker-deploy
Automatic docker deployments on git push
Last synced: 05 Nov 2024
https://github.com/baderlab/enrichmentmap_collection
Cytoscape Meta-App for the EnrichmetMap Pipline workflow.
Last synced: 05 Nov 2024
https://github.com/baderlab/domo-pred-human
Predicting SH3 domain mediated protein interactions in human
Last synced: 05 Nov 2024
https://github.com/baderlab/brendan_ccinxpred
Can intercellular signals be identified by transcriptional changes?
Last synced: 05 Nov 2024
https://github.com/baderlab/pawson-pub-graphs
A Cytoscape.js visualisation of the publication network of Tony Pawson
Last synced: 05 Nov 2024
https://github.com/baderlab/baderlab_static_webservers
repo with dockers for each of the static baderlab servers
Last synced: 05 Nov 2024
https://github.com/baderlab/netdx.examples
Companion data package for netDx
Last synced: 05 Nov 2024
https://github.com/baderlab/als_apa
Codes for APA-Net model and analysis for ALS APA atlas paper
Last synced: 05 Nov 2024
https://github.com/baderlab/brainapp
Biologically Relevant Analysis of Interaction Networks(Brain) Cytoscape App
Last synced: 05 Nov 2024
https://github.com/baderlab/powclui
POW! PDZ domain-peptide interaction prediction command line user interface
Last synced: 05 Nov 2024
https://github.com/baderlab/enrichmentmap_protocol
updated version of Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap Protocol as bookdown
Last synced: 05 Nov 2024
https://github.com/baderlab/summexpdr
Wrapper for SummarizedExperiment Objects for performing data integration + dimensionality reduction
Last synced: 05 Nov 2024
https://github.com/baderlab/sc_variant_profiler
A variant calling pipeline for single-cell RNAseq data
Last synced: 05 Nov 2024
https://github.com/baderlab/flash-mm
Fast and scalable LMM estimation algorithm for differential expression (DE) analysis of scRNA-seq
Last synced: 27 Nov 2024
https://github.com/baderlab/promoterpredictor
Using a SVM and 5 identified features, scan genomic coordinates for putative promoter regions
Last synced: 05 Nov 2024
https://github.com/baderlab/chan-covid19
Code for Chan lab collaboration for Covid-19 research
Last synced: 05 Nov 2024
https://github.com/baderlab/genemania_build
all scripts and code required to build Genemania database
Last synced: 05 Nov 2024