differential-expression-analysis

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

A comprehensive quality-control and quantification RNA-seq pipeline

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

A Python package for mechanism-aware single-cell differential analysis. It partitions DE genes into transcription-driven versus stabilization-driven classes using nascent (unspliced) RNA residuals. Also supports conventional DE, functional enrichment (ORA, GSEA, GO, KEGG), and visualization.

crispyx is a Python package for scalable CRISPR and Perturb-seq screen analysis on disk-backed AnnData files. It provides streaming quality control, normalization, pseudobulk aggregation, and differential expression without loading the full count matrix into memory.

A library for differential expression and gene set enrichment analysis based on hydra and pydantic.

A hybrid Python-R proteomics DEA package

Method of Combined P-value to identify Differential Expressed Gene in dataset

Plant miRNA discovery and functional annotation pipeline from small RNA-seq data

Integrated analysis of normal, ER+, HER2+, TNBC and metastatic breast cancer single-cell transcriptomes to identify cell populations, epithelial tumor states and subtype-specific programs.

Difference test with Gene expression by permutation method( by T-test and median test)