What is needed: Gene annotation as GTF
file for human and mouse.
We use the one from GENCODE: https://www.gencodegenes.org/
library('tidyverse')
gtf <- rtracklayer::import('gencode.v27.annotation.gtf')
t <- gtf %>%
as_tibble() %>%
select(gene_id, havana_gene, gene_name, gene_type) %>%
rename(
gencode = gene_id,
havana = havana_gene,
symbol = gene_name,
type = gene_type
) %>%
mutate(ensembl = gsub(gencode, pattern = '\\.[0-9]{1,3}', replacement = '')) %>%
distinct() %>%
select(gencode, ensembl, havana, symbol, type)
write_tsv(t, 'hg38_gene_ID_name.tsv.gz')
library('tidyverse')
gtf <- rtracklayer::import('gencode.vM16.comprehensive.CHR.gtf')
t <- gtf %>%
as_tibble() %>%
select(gene_id, havana_gene, gene_name, gene_type) %>%
rename(
gencode = gene_id,
havana = havana_gene,
symbol = gene_name,
type = gene_type
) %>%
mutate(ensembl = gsub(gencode, pattern = '\\.[0-9]{1,3}', replacement = '')) %>%
distinct() %>%
select(gencode, ensembl, havana, symbol, type)
write_tsv(t, 'mm10_gene_ID_name.tsv.gz')
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