annotables

July 6, 2025 · View on GitHub

Provides tables for converting and annotating Ensembl Gene IDs.

Installation

install.packages("devtools")
devtools::install_github("stephenturner/annotables")

Many bioinformatics tasks require converting gene identifiers from one convention to another, or annotating gene identifiers with gene symbol, description, position, etc. Sure, biomaRt does this for you, but I got tired of remembering biomaRt syntax and hammering Ensembl’s servers every time I needed to do this.

This package has basic annotation information from Ensembl Genes 114 for:

Human build 38 (grch38)
Human build 37 (grch37)
Mouse (grcm38)
Rat (rnor6)
Chicken (galgal5)
Worm (wbcel235)
Fly (bdgp6)
Macaque (mmul801)
Pig (Sscrofa11.1)
Dog (ROS_Cfam_1.0)
Zebrafish (GRCz11)

Where each table contains:

ensgene: Ensembl gene ID
entrez: Entrez gene ID
symbol: Gene symbol
chr: Chromosome
start: Start
end: End
strand: Strand
biotype: Protein coding, pseudogene, mitochondrial tRNA, etc.
description: Full gene name/description

Additionally, there are tx2gene tables that link Ensembl gene IDs to Ensembl transcript IDs.

Usage

library(annotables)

Look at the human genes table (note the description column gets cut off because the table becomes too wide to print nicely):

grch38

## # A tibble: 91,673 × 9
##    ensgene         entrez symbol chr     start    end strand biotype description
##    <chr>            <int> <chr>  <chr>   <int>  <int>  <int> <chr>   <chr>      
##  1 ENSG00000000003   7105 TSPAN6 X      1.01e8 1.01e8     -1 protei… tetraspani…
##  2 ENSG00000000005  64102 TNMD   X      1.01e8 1.01e8      1 protei… tenomodulin
##  3 ENSG00000000419   8813 DPM1   20     5.09e7 5.10e7     -1 protei… dolichyl-p…
##  4 ENSG00000000457  57147 SCYL3  1      1.70e8 1.70e8     -1 protei… SCY1 like …
##  5 ENSG00000000460  55732 FIRRM  1      1.70e8 1.70e8      1 protei… FIGNL1 int…
##  6 ENSG00000000938   2268 FGR    1      2.76e7 2.76e7     -1 protei… FGR proto-…
##  7 ENSG00000000971   3075 CFH    1      1.97e8 1.97e8      1 protei… complement…
##  8 ENSG00000001036   2519 FUCA2  6      1.43e8 1.44e8     -1 protei… alpha-L-fu…
##  9 ENSG00000001084   2729 GCLC   6      5.35e7 5.36e7     -1 protei… glutamate-…
## 10 ENSG00000001167   4800 NFYA   6      4.11e7 4.11e7      1 protei… nuclear tr…
## # ℹ 91,663 more rows

Look at the human genes-to-transcripts table:

grch38_tx2gene

## # A tibble: 412,044 × 2
##    enstxp          ensgene        
##    <chr>           <chr>          
##  1 ENST00000373020 ENSG00000000003
##  2 ENST00000612152 ENSG00000000003
##  3 ENST00000496771 ENSG00000000003
##  4 ENST00000494424 ENSG00000000003
##  5 ENST00000373031 ENSG00000000005
##  6 ENST00000485971 ENSG00000000005
##  7 ENST00000466152 ENSG00000000419
##  8 ENST00000371582 ENSG00000000419
##  9 ENST00000683048 ENSG00000000419
## 10 ENST00000371588 ENSG00000000419
## # ℹ 412,034 more rows

Tables are saved in tibble format, pipe-able with dplyr:

grch38 %>% 
    dplyr::filter(biotype == "protein_coding" & chr == "1") %>% 
    dplyr::select(ensgene, symbol, chr, start, end, description) %>% 
    head %>% 
    knitr::kable(.)

ensgene	symbol	chr	start	end	description
ENSG00000000457	SCYL3	1	169849631	169894267	SCY1 like pseudokinase 3
ENSG00000000460	FIRRM	1	169662007	169854080	FIGNL1 interacting regulator of recombination and mitosis
ENSG00000000938	FGR	1	27612064	27635185	FGR proto-oncogene, Src family tyrosine kinase
ENSG00000000971	CFH	1	196651754	196752476	complement factor H
ENSG00000001460	STPG1	1	24356999	24416934	sperm tail PG-rich repeat containing 1
ENSG00000001461	NIPAL3	1	24415802	24476735	NIPA like domain containing 3

Example with DESeq2 results from the airway package, made tidy with biobroom:

library(DESeq2)

## Loading required package: S4Vectors

## Loading required package: stats4

## Loading required package: BiocGenerics

## Loading required package: generics

## 
## Attaching package: 'generics'

## The following object is masked from 'package:dplyr':
## 
##     explain

## The following objects are masked from 'package:base':
## 
##     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
##     setequal, union

## 
## Attaching package: 'BiocGenerics'

## The following object is masked from 'package:dplyr':
## 
##     combine

## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs

## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique,
##     unsplit, which.max, which.min

## 
## Attaching package: 'S4Vectors'

## The following objects are masked from 'package:dplyr':
## 
##     first, rename

## The following object is masked from 'package:utils':
## 
##     findMatches

## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname

## Loading required package: IRanges

## 
## Attaching package: 'IRanges'

## The following objects are masked from 'package:dplyr':
## 
##     collapse, desc, slice

## Loading required package: GenomicRanges

## Loading required package: GenomeInfoDb

## Loading required package: SummarizedExperiment

## Loading required package: MatrixGenerics

## Loading required package: matrixStats

## 
## Attaching package: 'matrixStats'

## The following object is masked from 'package:dplyr':
## 
##     count

## 
## Attaching package: 'MatrixGenerics'

## The following objects are masked from 'package:matrixStats':
## 
##     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
##     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
##     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
##     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
##     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
##     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
##     colWeightedMeans, colWeightedMedians, colWeightedSds,
##     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
##     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
##     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
##     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
##     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
##     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
##     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
##     rowWeightedSds, rowWeightedVars

## Loading required package: Biobase

## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.

## 
## Attaching package: 'Biobase'

## The following object is masked from 'package:MatrixGenerics':
## 
##     rowMedians

## The following objects are masked from 'package:matrixStats':
## 
##     anyMissing, rowMedians

## The following object is masked from 'package:rlang':
## 
##     exprs

library(airway)

data(airway)
airway <- DESeqDataSet(airway, design = ~cell + dex)
airway <- DESeq(airway)

## estimating size factors

## estimating dispersions

## gene-wise dispersion estimates

## mean-dispersion relationship

## final dispersion estimates

## fitting model and testing

res <- results(airway)

# tidy results with biobroom
library(biobroom)

## Loading required package: broom

## Registered S3 methods overwritten by 'biobroom':
##   method      from 
##   glance.list broom
##   tidy.list   broom

res_tidy <- tidy.DESeqResults(res)

## Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
## ℹ Please use `tibble::as_tibble()` instead.
## ℹ The deprecated feature was likely used in the biobroom package.
##   Please report the issue at <https://github.com/StoreyLab/biobroom/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

head(res_tidy)

## # A tibble: 6 × 7
##   gene            baseMean estimate stderror statistic   p.value p.adjusted
##   <chr>              <dbl>    <dbl>    <dbl>     <dbl>     <dbl>      <dbl>
## 1 ENSG00000000003  709.      0.381     0.101     3.79   0.000152    0.00128
## 2 ENSG00000000005    0      NA        NA        NA     NA          NA      
## 3 ENSG00000000419  520.     -0.207     0.112    -1.84   0.0653      0.196  
## 4 ENSG00000000457  237.     -0.0379    0.143    -0.264  0.792       0.911  
## 5 ENSG00000000460   57.9     0.0882    0.287     0.307  0.759       0.895  
## 6 ENSG00000000938    0.318   1.38      3.50      0.394  0.694      NA

res_tidy %>% 
    dplyr::arrange(p.adjusted) %>% 
    head(20) %>% 
    dplyr::inner_join(grch38, by = c("gene" = "ensgene")) %>% 
    dplyr::select(gene, estimate, p.adjusted, symbol, description) %>% 
    knitr::kable(.)

gene	estimate	symbol	description
ENSG00000152583	-4.574919	SPARCL1	SPARC like 1
ENSG00000165995	-3.291062	CACNB2	calcium voltage-gated channel auxiliary subunit beta 2
ENSG00000120129	-2.947810	DUSP1	dual specificity phosphatase 1
ENSG00000101347	-3.766995	SAMHD1	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1
ENSG00000189221	-3.353580	MAOA	monoamine oxidase A
ENSG00000211445	-3.730403	GPX3	glutathione peroxidase 3
ENSG00000157214	-1.976773	STEAP2	STEAP2 metalloreductase
ENSG00000162614	-2.035665	NEXN	nexilin F-actin binding protein
ENSG00000125148	-2.210979	MT2A	metallothionein 2A
ENSG00000154734	-2.345604	ADAMTS1	ADAM metallopeptidase with thrombospondin type 1 motif 1
ENSG00000139132	-2.228903	FGD4	FYVE, RhoGEF and PH domain containing 4
ENSG00000162493	-1.891217	PDPN	podoplanin
ENSG00000134243	-2.195712	SORT1	sortilin 1
ENSG00000179094	-3.191750	PER1	period circadian regulator 1
ENSG00000162692	3.692661	VCAM1	vascular cell adhesion molecule 1
ENSG00000163884	-4.459128	KLF15	KLF transcription factor 15
ENSG00000178695	2.528175	KCTD12	potassium channel tetramerization domain containing 12
ENSG00000198624	-2.918436	CCDC69	coiled-coil domain containing 69
ENSG00000107562	1.911670	CXCL12	C-X-C motif chemokine ligand 12
ENSG00000148848	1.814543	ADAM12	ADAM metallopeptidase domain 12

Installation

Rationale

Usage