R toolkit for single cell genomics
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Dec 20, 2024 - R
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single-cell-genomics
Here are 98 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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Dec 20, 2024 - Python
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy
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Dec 16, 2024 - Python
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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May 21, 2024 - 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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Dec 14, 2024 - Python
Reference mapping for single-cell genomics
deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas
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Oct 27, 2024 - Jupyter Notebook
Community-provided extensions to Seurat
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Nov 22, 2024 - R
Single cell perturbation prediction
bioinformatics deep-learning generative-model scrna-seq transcriptomics single-cell single-cell-genomics
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Dec 5, 2024 - 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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Dec 20, 2024 - R
Single cell trajectory detection
markov-chain dimensionality-reduction scrna-seq trajectory-generation diffusion-maps differentiation manifold-learning single-cell-genomics cell-fate-transitions scrna-seq-analysis
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Nov 30, 2024 - Jupyter Notebook
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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Aug 21, 2024 - R
Interfaces for HDF5-based Single Cell File Formats
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Nov 4, 2023 - R
A Shiny web app for mapping datasets using Seurat v4
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Nov 5, 2024 - HTML
Convert Seurat objects to 10x Genomics Loupe files.
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Dec 12, 2024 - R
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
bioinformatics statistical-methods data-visualization dimensionality-reduction single-cell-genomics single-cell-rna-seq nonnegative-matrix-factorization single-cell-analysis single-cell-atac-seq
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Aug 2, 2023 - R
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
bioinformatics big-data genomics clustering scrna-seq graph-analytics memory-efficient tsne differential-expression umap dimension-reduction single-cell-genomics single-cell-rna-seq scalable-data-analysis single-cell-atac-seq multiomics cite-seq pseudotime scatac-seq gene-modules
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Dec 17, 2024 - Python
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
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Aug 14, 2024 - Python
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
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Dec 11, 2023 - Python
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