• UpdatedOct 18, 2022
• R

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

• UpdatedMar 17, 2025
• Nextflow

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

• UpdatedMar 6, 2025
• R

DEqMS is a tool for quantitative proteomic analysis

• UpdatedDec 11, 2024
• R

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

• UpdatedOct 17, 2024
• R

A quick recap of widely used differential analyses methods in R for RNA-seq experiments

• UpdatedDec 7, 2024

Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2

• UpdatedMay 7, 2021
• Jupyter Notebook

analyze_geo_microarrays.py : Differential expression analysis of published microarrays datasets from the NCBI Gene Expression Omnibus (GEO)

• UpdatedAug 1, 2021
• Python

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

• UpdatedMay 19, 2022
• R

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

• UpdatedDec 10, 2024
• R

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

• UpdatedMar 11, 2025
• R

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

• UpdatedFeb 8, 2024
• R

Bioinformatic analysis of gene expression microarray profiles and DGEs on R and R studio

• UpdatedFeb 26, 2025
• Jupyter Notebook

GSE147507 SARS-Cov-2 Dataset from Mt. Sinai

• UpdatedApr 4, 2020

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

• UpdatedJan 13, 2023
• R

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.

• UpdatedApr 17, 2023
• R

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.

• UpdatedFeb 27, 2023
• R

Tuberculosis@LOG and NPR, Macrophage gene expression time series.

• UpdatedOct 25, 2017
• Python

This repository showcases bioinformatics analysis and visualization results from an independent project for a scientific writing course, utilizing iDEP and a microarray dataset derived from NCBI GEO.

• UpdatedJan 7, 2025

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

• UpdatedAug 12, 2021
• R