Simple to use package for OMICS data analysis (featuring limma, WGCNA, GSEA)

Example analyses using recount

Workflow for Transcript, Gene, and Gene Set network analysis 🧬📊✨

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

A basic and quick workflow for differential expression analysis

This is the anonymized version of unpublished clinical RNAseq dataset analysis, serving as a reference for custom RNAseq analysis pipeline

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further in…

Enhancement the RNA simulator polyester to include polyA tails in the simulated sequences

Original version of the RNA-seq pipeline implemented in SPEAQeasy at https://github.com/LieberInstitute/SPEAQeasy.

Automated Isoform Discovery Detector (AIDD)

Gene co-expression network analysis

A web resource for studying the regulation of cassette exons by human splicing factors

RNA-seq Differential Gene Expression (DGE) analysis comparing multiple dataset samples involves the comparison of gene expression levels across multiple samples with the possibliity to account for defined conditions, treatments, or groups.

Repository for the analysis of spatial gene expression in molecular subtypes of Breast Cancer

A python package for working with inputs to and outputs from the toil-rnaseq pipeline

A prior learning and sampling model informed tool for learning with Single Cell RNA-Seq data

Jam R package suite for omics data analysis

Enhanced volcano plot using edgeR data