DEqMS is a tool for quantitative proteomic analysis

A Snakemake workflow and MrBiomics module for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea

EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.

A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.

This R script is used to analyze microarray data acquired by an Agilent SureScan Microarray Scanner.

Timeseries analysis of -omics data can be carried out by fitting spline curves to the data and using limma for hypothesis testing. For this, the right spline freedom and further hyperparameters must be identified, and the obtained hits clustered based on the spline shape.The R package SplineOmics streamlines this whole process and generates reports

Provides easy to use, objective oriented functions for preprocessing methylation data produced by an Illumina Infinium BeadChip and detecting differentially methylated positions and regions within the DNA.

This scripts involves five major steps including GEO dataset download, data normalization, data manipulation, fetching phenodata and feature data and differentially expressed genes (DEGs) analysis using R and bioconductor packages.

Methods overview with scripts looking at mtDNA and haplogroup association with CPTAC LUAD study.

Differential Gene Expression (DGE) Analysis in Curated Microarray Data of Breast Cancer Subtypes

Gene Expression analysis with BIG-DE

TCGA Colorectal Cancer RNA seq Data Analysis Pipeline

Performing RNA-seq data analysis with limma package