viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

A comprehensive pipeline for RNAseq data analysis

RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @cornell-TREX

CrusTome: A transcriptome database resource for large-scale analyses across Crustacea. Repository contains example script, links to database download, and supplementary files from manuscript.

A script used to calculate percent spliced-in (PSI) values from bulk RNA sequencing data.

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.

RNAseq pipeline examples

In development scripts for EvolOMICs group's NGS Data Analysis Pipeline

Pipeline to process RNAseq and ChIPseq data. Outputs include gene counts, transcripts per million, alternate splicing events, SNP calls, and bigwigs. Supports both Docker and Singularity for all dependencies.

A simple set of wrappers and tools for RNA-seq analysis. These tools were designed for the DSCI512 RNA-seq analysis class

Setup and testing for students

Full length example for SPEAQeasy

Tutorial for Genotyping by RNA Sequencing (GBRS), which quantifies transcripts via RNASeq and genotypes the samples using SNPs in transcripts.

A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)

Run RNASeq analysis with reference genome based on the Tophat-Cufflinks pipeline.

RNASeq and Call Variants