#Single-cell
Showing 38 of 38 repositories tagged #single-cell, ranked by stars
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
A tool for semi-automatic cell type classification
DANCE: a deep learning library and benchmark platform for single-cell analysis
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
Python package to perform enrichment analysis from omics data.
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
Generate high quality, publication ready visualizations for single cell transcriptomics data.
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
Convert between AnnData and SingleCellExperiment
Cluster single cells and analyze cell clade relationships with colorful visualizations.
Systematically learn and evaluate the latent geometry of high-dimensional data, with a focus on scRNAseq analysis
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
Bring your single-cell data to life
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
Spatial-Linked Alignment Tool
Deep learning for single-cell transcript counts
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Multi-sample Unified Discriminant ANalysis
A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
Iterative transfer learning with neural network improves clustering and cell type classification in single-cell RNA-seq analysis
ChatCell: Facilitating Single-Cell Analysis with Natural Language
Deprecated in favour of TopoMetry: https://github.com/davisidarta/topometry
MCP server for spatial transcriptomics analysis through natural language interfaces.
A Library for Denoising Single-Cell Data with Random Matrix Theory
Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
A generative model for phenotypic-based drug discovery