Tag: multivariate linear model pathway activity
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How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 17: Infer Signaling Pathway Activity with decoupleR and PROGENy
You already know the decoupleR engine from Part 16. Swap the network, swap one method, and you go from “which transcription factors are active” to “which signaling pathways are active” — in about half the code. In Part 16 you inferred per-cell transcription factor activity with decoupleR and CollecTRI, and the analysis landed on a…
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Recent Posts
- Bioinformatics Isn’t Dead. The Pipeline-Runner Is.
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- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 6: Footprinting Analysis
- How to Analyze Single-Cell ATAC-seq Data — A Complete Beginner’s Guide Part 5: Differential Accessibility Analysis
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Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression GSE282769 heatmap HOMER HPC Isoform limma MACS2 miRNA miRNA-seq MSigDB Normalization peak calling Pixi bioinformatics environment RNA-seq single-cell epigenomics beginners guide SLURM somatic mutations Transcript whole genome sequencing