Skills tagged "single-cell"

single-cell-multi-omics-integration - Single-cell multi-omics integration
single-cell multi-omics integration omicverse
★ 602 · Updated 2026-09-16
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
⚙ Integrate paired RNA and ATAC ⚙ Integrate unpaired data with GLUE ⚙ Perform SIMBA batch integration
scvelo - RNA Velocity Analysis for Single-Cell Data
single-cell RNA-seq trajectory inference bioinformatics
★ 5 · Updated 2026-06-30
Estimate cell state transitions from unspliced/spliced mRNA dynamics in single-cell RNA-seq data
⚙ load data ⚙ filter and normalize ⚙ compute moments
anndata - Annotated Data Matrix Management for Python
bioinformatics single-cell genomics data-structure
★ 422 · Updated 2026-06-30
Handle annotated data matrices with metadata in Python
⚙ create AnnData objects ⚙ read h5ad files ⚙ write h5ad files
anndata - Single-cell annotated data structure
data structure single-cell genomics bioinformatics
★ 97 · Updated 2026-06-30
Python package for handling annotated data matrices with efficient storage and manipulation
⚙ create AnnData objects ⚙ read h5ad files ⚙ write h5ad files
dynamo-pseudotime-velocity - RNA Velocity from Pseudotime
RNA velocity pseudotime vector field fate prediction
★ 502 · Updated 2026-06-15
Convert pseudotime to reusable RNA velocity outputs with vector field reconstruction
⚙ preprocess data ⚙ reduce dimension ⚙ compute neighbors
bio-single-cell-clustering - Single-Cell RNA-Seq Clustering Analysis
single-cell clustering bioinformatics dimensionality-reduction
★ 18 · Updated 2026-03-20
Perform dimensionality reduction and clustering on single-cell RNA-seq data using Seurat or Scanpy
⚙ Run PCA ⚙ Compute neighbors ⚙ Run Leiden clustering
bio-single-cell-clustering - Single-cell RNA-seq Clustering Analysis
single-cell RNA-seq clustering dimensionality-reduction
★ 602 · Updated 2026-03-20
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat and Scanpy
⚙ run PCA ⚙ compute variance ratio ⚙ visualize PCA
universal-single-cell-annotator - Universal Single-Cell Annotator for RNA-seq Data Annotation
genomics bioinformatics single-cell annotation
★ 18 · Updated 2026-02-12
Annotates single-cell RNA-seq data using marker genes, deep learning, or LLM reasoning
⚙ score cells with marker genes ⚙ transfer labels from celltypist ⚙ extract markers for LLM interpretation
sc-best-practices-auto - Single-cell Best Practices Collection with Auto Discovery
single-cell best-practices documentation automation
★ 3 · Updated 2026-02-11
Automatically discovers and collects single-cell analysis best practices documentation, HTML/MD files, and code blocks
⚙ discover directory indexes ⚙ crawl HTML files ⚙ collect MD documentation
sc-best-practices-auto - Single-Cell Best Practices Auto-Discovery Tool
single-cell bioinformatics documentation automation
★ 18 · Updated 2026-02-11
Automatically discovers and crawls single-cell analysis best practices documentation, HTML/MD files, and code blocks
⚙ discover documentation indexes ⚙ crawl HTML content ⚙ extract MD files