🧬 Analyze RNA-seq data of *Pseudomonas aeruginosa* SigX mutant vs. wild-type to uncover antibiotic stress-response pathways and transcriptional changes.

🧬 Analyze spatial gene expression in cancer tissues with this automated Python pipeline, uncovering insights into tumor microenvironments and biological regions.

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Annotated data.

An ontology of cell types

Transcriptome analysis of oilseed rape genotypes

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

pySeqRNA: a python-based package for RNASeq data analysis

National Microbiome Data Collaborative (NMDC) unified data model

Repository holding the code for the drugfindR R package

COmbinatorial Padlock-Probe-Amplified Fluorescence In Situ Hybridization

SNU-seq data processing and analysis scripts

Deconomix is a python toolbox for the deconvolution of bulk RNA profiles into their cellular composition.

Single-cell analysis in Python. Scales to >100M cells.

Python package to perform enrichment analysis from omics data.

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives

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

Pipeline to build a new human transcriptome, to annotate novel lncRNAs and to perform downstream analyses.

A multimodal analysis of Non-Small Cell Lung Carcinoma integrating semantic ontologies, structural bioinformatics, network medicine, and deep learning. This project bridges molecular and clinical data to identify novel drug targets (via AlphaFold & network proximity) and improve automated diagnosis using a custom CNN on X-ray classification.