Genomic Data Retrieval with R
R package providing query functionality to BioMart instances like Ensembl
A bioinformatics tool for analyzing somatic hypermutation
Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensembl dataset. Originally developed as part of a Masters in Bioinformatics project @ University of Exeter
Async pythonic interface to Biomart.
Make simple requests to Ensembl BioMart database.
Scripts for .bed file genomic region annotation with various tools
Historical Python/Ensembl REST and later R/BioMart analyses associated with the 2017 PLOS ONE study on organismal complexity.
This repository contains a fully reproducible pipeline for prioritising candidate genes and pathways from GWAS summary statistics using integrative pGWAS functional annotation to identify the most compelling targets for asthma
Visualization and further analyses of transcriptomic data analyzed by the MPI-Age Flaski RNAseq pipeline (with DESeq2) and proteomic data analyzed by MaxQuant (with limma)
Singularity container for running gene ontology anlaysis
Transcriptome Analysis of Heat and Drought-Stressed Wheat
Orthologs Databases — Archive of bioinformatics databases and PHP processing pipelines for cross-species ortholog analysis across 7 model organisms (2012-2016). Integrates data from 21 sources including HomoloGene, InParanoid, OrthoMCL, eggNOG, BioGRID, STRING, Gene Ontology, KEGG, and Reactome.
R-package: wrapper for {biomaRt} functions
Raw scripts for annotation, Venn, heatmap, STRINGdb, and machine learning (ML) workflows.
A collection of Jupyter notebooks for basic analysis of the data from the "BeatAML" study by Tyner et al. (2018)
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