R-Peridot

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.

Point and click, cross platform suite for analysing and visualizing next-generation sequencing datasets.

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Curated library of 550+ medical research agent skills spanning evidence insights, protocol design, omics/clinical data analysis, and academic writing; each skill is reviewed through MedSkillAudit and compatible with Claude Code, Codex, Open Code, OpenClaw, and SKILL.md-compatible agents (AIPOCH, 1.2K+ stars, MIT License, 2026)