R toolkit for single cell genomics
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Dec 20, 2024 - R
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single-cell-rna-seq
Here are 409 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
🐟 🍣 🍱 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 10x single-cell-rna-seq selective-alignment rna-seq-quantification
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May 29, 2024 - C++
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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Sep 5, 2024 - R
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
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Dec 20, 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
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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Dec 20, 2024 - Python
Table of software for the analysis of single-cell RNA-seq data.
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Dec 20, 2024 - R
Multi-subject Single Cell Deconvolution
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Mar 4, 2024 - R
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
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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Feb 27, 2024 - JavaScript
R package for the joint analysis of multiple single-cell RNA-seq datasets
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Feb 26, 2024 - R
Differential expression analysis for single-cell RNA-seq data.
bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq
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May 30, 2023 - Python
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
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Sep 24, 2024 - R
LIANA+: an all-in-one framework for cell-cell communication
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Sep 21, 2024 - Python
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
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Dec 20, 2024 - Rust
Haplotype-aware CNV analysis from single-cell RNA-seq
cancer-genomics single-cell phylogeny single-cell-rna-seq single-cell-analysis cnv-detection spatial-transcriptomics lineage-tracing
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Dec 5, 2024 - R
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
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