| Title: | Human Gene Annotation Data from 'Ensembl' |
| Version: | 1.0.0 |
| Description: | Gene information from 'Ensembl' genome builds 'GRCh38.p14' and 'GRCh37.p13' to use with the 'topr' package. The datasets were originally downloaded from https://ftp.ensembl.org/pub/current/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.gtf.gz and https://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz and converted into the format required by the 'topr' package. See https://github.com/totajuliusd/topr?tab=readme-ov-file#how-to-use-topr-with-other-species-than-human to see the required format. |
| License: | LGPL (≥ 3) |
| Encoding: | UTF-8 |
| LazyData: | true |
| LazyDataCompression: | xz |
| RoxygenNote: | 7.2.3 |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown, markdown |
| Config/testthat/edition: | 3 |
| Depends: | R (≥ 3.5.0) |
| NeedsCompilation: | no |
| Packaged: | 2024-01-31 10:59:17 UTC; tota |
| Author: | Thorhildur Juliusdottir [cph, aut, cre] |
| Maintainer: | Thorhildur Juliusdottir <totajuliusd@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-02-02 12:40:05 UTC |
enshuman
Description
Human gene annotation datasets to use with the 'topr' package
datasets
The two datasets are:
-
hg38Gene information from genome build GRCh38.p14 -
hg37Gene information from genome build GRCh37.p13
Examples
library(enshuman)
head(hg38)
head(hg37)
Ensembl genes build GRCh37.87
Description
wget https://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
Usage
hg37
Format
A data frame with 55,882 rows and 7 variables:
- chrom
chromosome
- gene_start
genetic position of gene start
- gene_end
genetic position of gene end
- gene_symbol
The name of the gene
- biotype
the biotype of the gene
- exon_chromstart
genetic positions of exon start
- exon_chromend
genetic position of exon end
Ensembl genes build GRCh38.111
Description
wget https://ftp.ensembl.org/pub/current/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.gtf.gz
Usage
hg38
Format
A data frame with 41,016 rows and 7 variables:
- chrom
chromosome
- gene_start
genetic position of gene start
- gene_end
genetic position of gene end
- gene_symbol
the name of the gene
- biotype
the biotype of the gene
- exon_chromstart
genetic positions of exon start
- exon_chromend
genetic position of exon end