R toolkit for single cell genomics
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Aug 28, 2026 - R
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single-cell-rna-seq
Here are 620 public repositories matching this topic...
Deep probabilistic analysis of single-cell and spatial omics data
deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse
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Sep 2, 2026 - Python
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish single-cell-rna-seq selective-alignment rna-seq-quantification
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Sep 2, 2026 - Rust
NicheNet: predict active ligand-target links between interacting cells
rna-seq gene-expression network-inference data-integration single-cell-rna-seq single-cell-omics intercellular-communication ligand-receptor ligand-target cell-cell-communication
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Jun 1, 2026 - R
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
scrna-seq shiny-apps single-cell shinyapps single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat single-cell-omics scrna-seq-analysis single-cell-sequencing shiny-app scanpy scatac-seq anndata scrna-pipeline seurat-objects single-cell-pipeline
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Mar 11, 2026 - R
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy scverse
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Aug 31, 2026 - Python
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May 26, 2026 - R
CellRank: dynamics from multi-view single-cell data
data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions fuzzy-clustering-analyses rna-velocity cell-fate-determination
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Aug 31, 2026 - Python
DANCE: a deep learning library and benchmark platform for single-cell analysis
python data-science benchmark machine-learning bioinformatics deep-learning computational-biology dance single-cell multimodality single-cell-rna-seq graph-neural-networks spatial-transcriptomics single-cell-rna-sequencing
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Aug 31, 2026 - Python
Table of software for the analysis of single-cell RNA-seq data.
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Sep 2, 2026 - R
scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.
visualization spatial-data spatial-data-analysis single-cell-rna-seq giotto single-cell-analysis seurat single-cell-sequencing scanpy
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Aug 28, 2026 - HTML
Papers with code for single cell related papers
reproducible-research reproducible-science scrna-seq single-cell single-cell-rna-seq single-cell-atac-seq single-cell-omics scrna-seq-analysis paper-with-code
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Mar 23, 2026
LIANA+: an all-in-one framework for cell-cell communication
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Sep 1, 2026 - Python
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
visualization ggplot2 customization scrna-seq single-cell single-cell-genomics single-cell-rna-seq seurat
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Jun 30, 2026 - R
Multi-subject Single Cell Deconvolution
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Mar 4, 2024 - R
Tutorial for scRNA-seq data analysis beginners using R
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Mar 5, 2025
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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Jun 28, 2026 - JavaScript
Generate high quality, publication ready visualizations for single cell transcriptomics data.
visualization ggplot2 r data-visualization rstats single-cell single-cell-genomics single-cell-rna-seq publication-quality-plots seurat
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Mar 2, 2026 - R
R package for the joint analysis of multiple single-cell RNA-seq datasets
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Jul 2, 2026 - R
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
cancer-genomics single-cell phylogeny single-cell-rna-seq single-cell-analysis single-cell-atac-seq cnv-detection single-cell-omics spatial-transcriptomics lineage-tracing
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Feb 4, 2026 - R
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