Clustering scRNAseq by genotypes
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- Python
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scrnaseq
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An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
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This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
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Systematically learn and evaluate the latent geometry of high-dimensional data, with a focus on scRNAseq analysis
visualization data-science machine-learning graph clustering scikit-learn data-visualization dimensionality-reduction single-cell graph-layout manifold-learning scrnaseq laplace-beltrami hypothesis-generation scrnaseq-analysis
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a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
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Cell type pipes for R
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- R
Explore and share your scRNAseq clustering results
r ui shiny scrna-seq single-cell differential-expression clustering-evaluation scrnaseq scrna-seq-analysis
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R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.
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Differential expression and allelic analysis, nonparametric statistics
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Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing
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Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq
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R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
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Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.
r scrna-seq single-cell scrnaseq single-cell-genomics seurat immune-system immune-repertoire clonal-analysis
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Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
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A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and statistically enriched covariation of gene programs between interacting cell types from the neighborhood.
scrna-seq scrna-seq-data scrnaseq nico scrna-seq-analysis spatial-transcriptomics niche-modelling merfish seqfish niche-covariation
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- Jupyter Notebook
Seurat v5 compatible HDF5 converter for single-cell data — h5ad, h5Seurat, h5mu, Loom with full spatial data support
bioinformatics hdf5 r-package scrnaseq single-cell-genomics single-cell-rna-seq seurat spatial-transcriptomics anndata h5ad mudata seurat-v5 h5mu
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This repository stores the scigenex R library.
r classification scrna-seq r-package unsupervised-learning scrnaseq scrna-seq-analysis filtering-algorithm
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- R
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