TMEM

Repository and package for bioinformatics- and molecular biology-related functions, facilitating biological data exploration and easier plotting of downstream NGS analyses (heatmaps, bargraphs, volcano plots, MA plots, scatter plots)

Adapted from source code used to analyze data in Dr. Martha Bhattacharya's lab at the University of Arizona

• The lab studies transmembrane protein 184b (TMEM184B), a protein involved in axon degeneration and cancer, across multiple neuroscience model systems

This package contains functions for:

• gathering gene ontology information for streamlined downstream bioinformatics plotting
• gathering orthologous gene and alias information
• gathering the genes and specific gene ontology terms associated with a generic gene ontology
• extracting a Z-score matrix from a transcriptional profile dataframe for plotting heatmaps

Three publications involved the use of these functions in this package (TMEM) and each of these publications have (or will have) their own repositories (eriklarsen4/Itch, eriklarsen4/Endo, and eriklarsen4/Hippo coming soon). Please see those repositories for each paper's respective URL.

Included data for the TMEM package is derived from the publicly available "itch paper." All of that publication's genomics and Calcium imaging data, analyses, and code are contained within the eriklarsen4/Itch repository. Please visit that repository for more detail.

These functions were developed, in-house, years before any Bioconductor APIs were developed. The goal was to integrate downstream analytical results (pathway analysis, gene ontology, networks, etc., from e.g. PANTHER or KEGG) to DEA and GSEA results files for mapping-- for visualizing results without downloading more files, manually transcribing results, or creating extra plots. I have not yet compared the functionality between Bioconductor/GO.db with this package.

Please see the vignette for more detail.

Coming soon to this repository are whole-transcriptome sequencing (WTS) and whole-exome sequencing (WES) tutorials, along with a Markdown with examples for building a Shiny app, with a link to the example app.