Transcriptome analysis of oilseed rape genotypes

Repository holding the code for the drugfindR R package

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

Computational biology functions I made to help in my analyses.

MMP3C v2: A Method to Evaluate Pairwise Metabolic Plasticity

An R package providing tools for single-cell RNA-seq data analysis, enhancing existing methods with helper functions.

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Visualization and exploration of SummarizedExperiment objects from the DoReMiTra collection

Revealing Biological Insights for Imaging-Derived Phenotypes through Transcriptomic Enrichment

Reproducible WGCNA pipeline for PCOS microarray dataset GSE48301

Process RatGTEx pipeline results into data files for the RatGTEx site

RNA Seq Course materials as part of the ACE_Uganda bioinformatics course, Spring 2021

Nextflow pipeline for microarray and RNA-seq

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

This workflow uses Kallisto to quickly count transcript levels from RNA-Seq data and then analyzes those counts using the web platform NetworkAnalyst to find the biological pathways affected.

An interactive R Shiny app for RNA-seq analysis. Upload a counts matrix and phenotype data to perform differential expression, feature selection (via Random Forest), and pathway enrichment. Generate PCA, UMAP, volcano plots, heatmaps, and enrichment barplots — all without writing a single line of code.

Orchestrating Blood Radiation Transcriptomic Data

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

RNA-seq Quality Control and Preprocessing Tool - Interactive Shiny application for comprehensive RNA sequencing data validation, quality assessment, filtering, and normalization. Developed at Harvard Medical School Department of Immunology for global research use.

Reference-guided transcript discovery and quantification for long read RNA-Seq data