CompBio, AI/ML

cellxgene_VIP. Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

Quickomics. Quickomics: exploring omics data in an intuitive, interactive and informative manner. Bioinformatics. 2021 Apr 26:btab255.

ScaleSC. ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU. https://doi.org/10.1093/bioadv/vbaf167

xOmicsShiny. xOmicsShiny: an R Shiny application for cross-omics data analysis and pathway mapping, Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf097.

scRNAsequest. scRNASequest: an ecosystem of scRNA-seq analysis, visualization and publishing. BMC Genomics 24, 228 (2023).

CellDepot. CellDepot: A unified repository for scRNA-seq data and visual exploration. J Mol Biol. 2021 Dec 28:167425. doi: 10.1016/j.jmb.2021.167425.

RNASequest. R

CompBioAgent. CompBioAgent: An LLM-powered agent for single-cell RNA-seq data exploration. https://doi.org/10.1101/2025.03.17.643771

OmicsView. OmicsView: omics data analysis through interactive visual analytics

CellMap. R

SpaceSequest. R

bioInfograph. bioInfograph: an online tool to design and display multi-panel scientific figure interactively

FundusNet. FundusNet: A Deep-Learning Approach for Fast Diagnosis of Neurodegenerative and Eye Diseases Using Fundus Images.

scRNAseq_DE. R

Mouse_Cuprizone_Spatial. R

cellxgene. An interactive explorer for single-cell transcriptomics data

SpliceHarmonization. Splice Result Harmonization from Multiple Methods

awesome-single-cell. List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

whitepapers. Deep Learning Best Practices

ZSF1. High resolution molecular and histological analysis of renal disease progression in ZSF1 (fa/fa cp) rats, a model of type 2 diabetic nephropathy

HSCTGFB. STAT3 activation is central to TGF-β1 mediated primary human hepatic stellate cell activation

python-cheatsheet. Comprehensive Python Cheatsheet

SpatialSC_vis. Jupyter Notebook

CSFinMS. Integrated single cell transcriptomics of cerebrospinal fluid cells in early Multiple Sclerosis