R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
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Jan 6, 2024 - R
#
single-cell-analysis
Here are 254 public repositories matching this topic...
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
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
single-cell-analysis spatial-transcriptomics cell-cell-interaction cell-cell-communication microenvironment
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Mar 4, 2026 - R
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
visualization python bioinformatics heatmap plot pandas matplotlib single-cell-analysis complex-heatmaps data-visualization-python complexheatmap clustermap
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Sep 1, 2026 - Python
Community-provided extensions to Seurat
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Jun 29, 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
Analysis Pipeline for Single Cell ATAC-seq
machine-learning-algorithms sequencing epigenetics bioinformatics-pipeline single-cell-analysis single-cell-atac-seq
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Apr 27, 2023 - R
🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
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Apr 26, 2026 - Python
Tutorial for scRNA-seq data analysis beginners using R
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Mar 5, 2025
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
PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.
react opencv bioinformatics-pipeline microbiology bacteria fluorescence-microscopy-imaging cell-analysis single-cell-analysis fastapi nikon-nd2 cell-contour
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Sep 5, 2026 - Python
List of Spatial Transcriptomics related Tools organized per category
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Aug 17, 2026 - Python
This repository contains scNotebooks, a collection of interactive Jupyter and Google Colab notebooks designed to teach and practice single‑cell and spatial transcriptomics. The notebooks guide learners through the complete workflow from introductory steps and single‑cell pipelines to diverse analytical approaches, and FAIR and sharing data
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Sep 5, 2026 - Jupyter Notebook
Context specific and dynamic gene regulatory network reconstruction and analysis
network-inference network-visualization network-analysis single-cell-analysis gene-regulatory-network dynamic-network single-cell-multiomics single-cell-network
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Aug 3, 2026 - Python
A collection of 50+ trajectory inference methods within a common interface 📥📤
bioinformatics-algorithms single-cell-rna-seq single-cell-analysis trajectory-inference-methods trajectory-inference pseudotemporal-ordering
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Dec 21, 2023 - R
Cluster single cells and analyze cell clade relationships with colorful visualizations.
visualization bioinformatics-pipeline single-cell bioinformatics-algorithms single-cell-rna-seq single-cell-analysis
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Oct 28, 2024 - Haskell
R package to visualize gene expression data based on weighted kernel density estimation
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Feb 6, 2026 - R
Spatial Single-Cell Analysis Toolkit
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Sep 3, 2026 - Python
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