GeneAnnotationsR

Package for getting gene-level annotations in R.

Firstly, all the protein coding genes are needed

• A function called 'get_protein_coding_genes()' gets a df of all protein coding genes HGNC IDs.

List of gene annotations:

Constraint metrics

• Alphamissense

• Gnomad constraint metrics

• Shet metrics

• DOMINO metric

• SCoNes metric

Cell line screens gene essentiality

• Cancer cell line (DepMap) screen gene essentiality

• hPSC screen gene essentiality

Mouse model gene essentiality

• Mouse (MGI + IMPC) gene viability

Phenotype

• Mouse and zebrafish Phenodigm scores (only available for NDD and cardiac rare disease genes)

Interactions

• Chemical-gene interactions

Gene sequence

• Gene expression (human and mouse, evodevo group)

• Gene sequence annotations (gene length, coding sequence length, 3' and 5' UTR length)

• De novo mutation rates (synonymous, missense, loss-of-function, splice site, nonsense, and all) (https://pmc.ncbi.nlm.nih.gov/articles/PMC4222185/)

Protein

• Protein expression

• Sub-cellular location

• GO terms

Other functions available:

• for summary stats, plotting

Requirements:

• BiocManager

• biomaRt

• dplyr

• readr

• tibble

• data.table

• magrittr

• tidyr

• org.Hs.eg.db

• AnnotationDbi

• GO.db

Example:

Check rmarkdown.