Deconvoluting mouse Immune cell fractions from Bulk RNAseq data with ImmuCell-AI_mouse

analysis of RNA-seq data

Clustering is a common exercise to determine how closely samples are related to each other. This shows how samples can be clustered using a PCoA and PCA and visualizing using ggplot. Particularly, how to cluster RNA-seq samples.

This is a script I used to make an R Shiny application that allows for browsing the time-course gene expression signal, and associated statistics, for an experiment where MCF-7 cells were exposed to oxidative stress-inducing compounds. This dataset was published in *Free Radical Biology and Medicine*, article found here https://doi.org/10.1016/j…

Automated Isoform Discovery Detector (AIDD)

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.

An R package to parse and manage text output of the sequencing quality control utility (fastQC)

Template for RNASeq analyses running on HPCC

Snakemake workflow for Bulk RNASeq at both genome level and transcripts level.

Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.

To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.

Creating a simple mirrorplot can be good visualization for showing up/down regulated genes in an RNA-seq. This details how to create a mirrorplot using ggplot2.

Differential expression analysis in R for RNA sequence reads of fission yeast.

Bioc2022 workshop. SEESAW: Statistical Estimation Of Allelic Expression Using Salmon And Swish

RNAseq scripts

IMOM - A pipeline for interacting with, processing, and analyzing multi-OM datasets in phylogenetic and evolutionary context

An R package which stores the code used to process Long Life Family Study RNA sequencing from fastq to analysis releases

Advanced bioinformatics analysis of RNA sequencing data and genomic databases using R. Explore allelic imbalances, SNP variants, and phylogenetic trees to uncover genetic insights and visualize complex data interactions.

This repository is the current repository for our Jones et al. 2024 manuscript titled Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage.

Useful wrappers and functions for RNA-Seq analysis