R toolkit for single cell genomics
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Feb 14, 2025 - R
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human-cell-atlas
Here are 53 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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Feb 24, 2025 - 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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Jan 11, 2025 - Jupyter Notebook
starfish: unified pipelines for image-based transcriptomics
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Feb 24, 2025 - Python
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
visualization gui shiny clustering gene-expression feature-extraction transcriptomics single-cell hacktoberfest dimension-reduction human-cell-atlas
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Dec 10, 2024 - R
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
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Jun 28, 2021 - R
A tool for unsupervised projection of single cell RNA-seq data
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Nov 24, 2020 - R
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
This contains the dataset for comparing scRNA-seq analysis methods
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Aug 26, 2020 - HTML
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
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Dec 18, 2024 - R
Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.
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Nov 9, 2024 - R
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
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Feb 24, 2025 - Ruby
Bayesian MCMC matrix factorization algorithm
machine-learning bioinformatics bayesian-inference single-cell-rna-seq non-negative-matrix-factorization human-cell-atlas
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Feb 10, 2025 - C++
Aligning gene expression trajectories of single-cell reference and query systems
python scrna-seq dynamic-programming bayesian-inference single-cell human-cell-atlas pseudotime-trajectory trajectory-alignment minimum-message-length
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Oct 14, 2024 - Jupyter Notebook
Clone of the Bioconductor repository for the DropletUtils package.
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Dec 10, 2024 - R
Tutorials, workflows, and convenience scripts for Single Cell Portal
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Mar 5, 2024 - HTML
Clone of the Bioconductor repository for the scran package.
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Sep 5, 2024 - R
A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
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Nov 16, 2021 - R
Access and Format Single-cell RNA-seq Datasets from Public Resources
geo bam fastq zenodo sra single-cell-rna-seq format-conversion-tool human-cell-atlas cellxgene panglaodb ucsc-cell-browser
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Dec 21, 2024 - R
This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
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Jun 24, 2024 - R
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