microarray

Cross-platform (Windows + Linux) no-code desktop app for reproducible bulk RNA-seq & microarray analysis: STAR/HISAT2/Salmon alignment, DESeq2/limma, GO/KEGG/g:Profiler enrichment, and STRING PPI networks — with first-class support for crops and fungi that lack a Bioconductor OrgDb.

Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)

Label-driven comparison of gene expression regions across measurement technologies. Microarray, bulk RNA-seq and single-cell in one question, local first, no API keys.

Python port of R limma for differential expression analysis

Genetic-embedded Nuclear Reaction Optimization with F-score filtering for gene selection in cancer classification. Published in IJMS 2025.

F-score filtering combined with Nuclear Reaction Optimization for gene selection in cancer classification. Methodology, datasets, and results from the CIMB 2025 paper.

Nuclear Reaction Optimization applied to gene selection in microarray cancer datasets. Implementation from the Diagnostics 2025 paper.

Collection of NGS analysis pipelines, transcriptomics, genomics, and bioinformatics workflows tried in R and Python

Unsupervised clustering and differential expression of GABAergic interneuron markers in postmortem DLPFC: schizophrenia vs. control (GSE53987)

Automated GEO dataset search, download, and preprocessing tool for gene expression meta-analyses

Differential Expression Analysis Pipeline

Genomic data manipulation tool

bioTEA - A user friendly tool to perform transcript expression analysis

extract experimental metadata from GEO xml files

Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.

A toolkit for navigating and analyzing gene expression datasets

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

Bioinformatics course project - Fall 2020, analysis of genetic expression omnibus (GEO) data series of Acute Myeloid Leukemia

A list of publicly available Microarray Gene Expression datasets with proper attribution and associated toolkits.