This repository is aimed to test the therapeutic utility of AutoCore endotypes pipeline

Cross-Species Tumor Transcriptomic Similarity Analysis R package

Isoform-level functional RNA-Seq analysis 🧬

Brings bulk and pseudobulk transcriptomics to the tidyverse

This repository is for our 2024 manuscript, Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model

Brings SummarizedExperiment to the tidyverse

Process RatGTEx pipeline results into data files for the RatGTEx site

Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.

Repository for analyses performed in "A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development" (doi.org/10.1101/2024.02.26.581612)

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

🧬 Toolkit for Evaluating Gene Sets as Phenotype Markers in R

An R package to perform differential network analysis in single and multi-omic data. It can also be used for feature selection in ML.

Easily install and load packages from the tidyomics ecosystem

Bio-informed QSAR framework integrating P. falciparum transcriptomic signatures with molecular descriptors for enhanced antimalarial activity prediction (6.1% improvement, 98.3% feature reduction)

Repository holding the code for the drugfindR R package

Molecular interactions inference from single-cell multi-omics data

RNA-seq analysis of Isl1 knockout vs wild-type mouse allantois (GSE247182) using DESeq2 and fgsea for pathway enrichment.

Peripheral heterogeneity of claudin-low breast cancer

R/shiny interface for interactive visualization of data in SummarizedExperiment objects