differential-expression

Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Single-cell perturbation analysis

Differential expression analysis for single-cell RNA-seq data.

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Brings bulk and pseudobulk transcriptomics to the tidyverse

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

integrated RNA-seq Analysis Pipeline

R package for pathway analysis in scRNA-seq data

Volcano plots for differential expression in R. Reads DESeq2, edgeR and limma output directly; highlight genes of interest and compose gene tables with gt.

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Porting DESeq2 into python via rpy2

Compare different differential abundance and expression methods

Explore and share your scRNAseq clustering results

Experimental design framework for scRNAseq population studies (eQTL and DE)

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

An R package to plot interactive three-way differential expression analysis

pseudobulking on an AnnData object

interactive plots for differential expression analysis