Skills tagged "RNA-seq"

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
bio-geo-data - Query NCBI GEO Expression Datasets
bioinformatics gene expression NCBI GEO
★ 15 · Updated 2026-06-30
Query and access NCBI Gene Expression Omnibus datasets using Biopython Entrez module
⚙ search GEO datasets ⚙ fetch GEO summaries ⚙ get FTP links
biomni - Biomedical AI Research Agent Framework
biomedical AI agent genomics drug discovery
★ 422 · Updated 2026-06-15
Autonomous AI framework for biomedical research tasks including genomics, drug discovery, and clinical analysis
⚙ decompose biomedical tasks ⚙ generate analysis code ⚙ execute analysis pipelines
biomni - Biomedical AI Agent Framework
biomedical genomics drug discovery molecular biology
★ 602 · Updated 2026-06-15
Autonomous biomedical AI agent for genomics, drug discovery, molecular biology, and clinical analysis tasks
⚙ execute biomedical queries ⚙ decompose research tasks ⚙ retrieve biomedical knowledge
sc-qc - Single-cell QC metrics calculation and visualization
singlecell quality control QC metrics visualization
★ 83 · Updated 2026-03-26
Calculate QC metrics and generate diagnostic plots for single-cell RNA-seq data
⚙ calculate QC metrics ⚙ load AnnData object ⚙ generate violin plots
bio-splicing-pipeline - RNA-seq Alternative Splicing Analysis Pipeline
alternative splicing RNA-seq differential analysis bioinformatics
★ 1,207 · Updated 2026-03-25
End-to-end alternative splicing analysis from FASTQ to differential splicing results
⚙ Trim FASTQ reads ⚙ Align RNA-seq reads ⚙ Perform junction QC
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
bulk-rna-seq-batch-correction-with-combat - Harmonize bulk RNA-seq data across batches with ComBat
RNA-seq batch-correction data-harmonization bioinformatics
★ 18 · Updated 2026-02-23
Remove batch effects from merged bulk RNA-seq or microarray cohorts using omicverse's pyComBat wrapper
⚙ Load expression matrices ⚙ Concatenate datasets by shared genes ⚙ Run ComBat batch correction
bulk-rna-seq-batch-correction-with-combat - Bulk RNA-seq batch correction with ComBat
RNA-seq batch correction data harmonization bioinformatics
★ 1,209 · Updated 2026-02-23
Remove batch effects from merged bulk RNA-seq or microarray cohorts using omicverse's pyComBat wrapper
⚙ read expression matrices ⚙ concatenate gene expression data ⚙ run ComBat batch correction