interactivereport

CompBio, AI/ML's repositories

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.

Language:Jupyter NotebookMIT159 6 105

Quickomics

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

Language:R42 6 7

ScaleSC

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

Language:PythonMIT36 50

xOmicsShiny

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

Language:RMIT34 2 13

scRNAsequest

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

Language:R26 5 3

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.

Language:JavaScript24 6 4

RNASequest

Language:R18 6 34

CompBioAgent

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

Language:SCSSMIT16 30

OmicsView

OmicsView: omics data analysis through interactive visual analytics

Language:HTMLMIT16 30

CellMap

Language:R15 3 3

bioInfograph

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

Language:HTMLMIT1100

scRNAseq_DE

Language:RNOASSERTION8 4 1

SpaceSequest

Language:RMIT700

cellxgene

An interactive explorer for single-cell transcriptomics data

Language:JavaScriptMIT500

FundusNet

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

Language:Jupyter NotebookMIT5 40

Mouse_Cuprizone_Spatial

Language:RMIT5 10

awesome-single-cell

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

MIT300

HSCTGFB

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

Language:HTML200

ZSF1

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

Language:HTML200

CSFinMS

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

1 10

python-cheatsheet

Comprehensive Python Cheatsheet

Language:Python100

SpatialSC_vis

Language:Jupyter Notebook100

SpliceHarmonization

Splice Result Harmonization from Multiple Methods

Language:PythonMIT100

iSCALE

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms

Language:PythonNOASSERTION000

QuickRNASeq

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization

Language:HTML000

rpy2

Interface to use R from Python

Language:PythonGPL-2.0000

scRNA-seq_notes

A list of scRNA-seq analysis tools

Language:RMIT000

TransgeneSeq

Benchmarking and optimization of a high-throughput sequencing based method for transgene sequence variant analysis in biotherapeutic cell line development

Language:R000

whitepapers

Deep Learning Best Practices

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