Bioinformatics Tools

Tool Description Update/Version URL
SciMiner Web-based literature mining tool for gene/protein extraction and enrichment. System migration (04/19/2016) http://hurlab.med.und.edu/SciMiner/
PubChemSR Stand-alone program for data retrieval from NCBI PubChem databases. v3.6.4 (12/18/2019) https://sourceforge.net/projects/pubchemsr/
DNMKB2 Repository and analysis portal for diabetic neuropathy transcriptomics data (140 DEG sets). v2.1 (10/21/2018) http://hurlab.med.und.edu/DNMKB2/
VennDetail Bioconductor R package for Venn–Pie plots and subset extraction (up to 8 sets). v1.10.0 (02/10/2022) http://hurlab.med.und.edu/VennDetail / https://github.com/hurlab/VennDetail
richR Functional enrichment and visualization R package. Updated 01/20/2025 http://hurlab.med.und.edu/richR / https://github.com/hurlab/richR
Tox21 Enricher Online enrichment tool for Tox21 chemical screening data; R version available. v2.4.0 (04/25/2023) http://hurlab.med.und.edu/Tox21Enricher / https://github.com/hurlab/tox21enricher
richStudio R Shiny app for enrichment and clustering analyses. v0.0.5 (01/07/2024; in development) http://hurlab.med.und.edu:3838/richStudio/ https://github.com/hurlab/richStudio
richCluster C++-based hierarchical clustering algorithm wrapped in R. v1.0.0 (10/4/2025; submitted to CRAN) https://github.com/hurlab/richCluster
scGEN Gene-aware embedding network for single-cell RNA-seq clustering. Ongoing (10/5/2025) https://github.com/hurlab/scGEN