if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("biomaRt", version = "3.8")
library(biomaRt)
listMarts()
listEnsembl()
browseVignettes("biomaRt")
listMarts(host="plants.ensembl.org")

Homodb<-useMart(dataset="hsapiens_gene_ensembl",biomart='ensembl')
plantdb <- useMart(dataset="atauschii_eg_gene",biomart='plants_mart')
listDatasets(useMart(host="plants.ensembl.org", biomart='plants_mart', verbose = FALSE))

seq1 = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = Homodb)

seq2 = getSequence(id="211550_at", type="affy_hg_u95av2",seqType="cdna", upstream = 20, mart = Homodb)
seq2

getGene(id="211550_at", mart = Homodb)

affyids=c("211550_at", "202431_s_at", "206044_s_at")
getBM(attributes=c('affy_hg_u133_plus_2', 'ensembl_gene_id'),
      filters = 'affy_hg_u133_plus_2',
      values = affyids,
      mart = Homodb)
searchFilters(mart = Homodb, pattern = "ensembl.*id")

affyids=c("202763_at","209310_s_at","207500_at")
getBM(attributes = c('affy_hg_u133_plus_2', 'hgnc_symbol', 'chromosome_name',
                     'start_position', 'end_position', 'band'),
      filters = 'affy_hg_u133_plus_2',
      values = affyids,
      mart = Homodb)
entrez=c("1956","4609", "673")
goids = getBM(attributes = c('entrezgene', 'go_id'),
              filters = 'entrezgene',
              values = entrez,
              mart = Homodb)
head(goids)
go=c("GO:0000902","GO:0000080","GO:0000114","GO:0004714")
chrom=c(9, 7,20,"Y")
getBM(attributes= "hgnc_symbol",
      filters=c("go","chromosome_name"),
      values=list(go, chrom), mart=Homodb)


miRNA <- getBM(c("mirbase_id", "ensembl_gene_id", "start_position", "chromosome_name"), filters=c("chromosome_name", "with_mirbase"), values=list(13, TRUE), mart=Homodb)
miRNA


go=c("GO:3400000","GO:36500000")
chrom=c(9)

ids = getBM(attributes= c("affy_hg_u133_plus_2", "ensembl_gene_id", "start_position", "end_position"),
            filters=c("chromosome_name", "start", "end"),
            values=list(chrom, 3400000, 36500000), mart=Homodb)
a <- ids$end_position-ids$start_position

hist(a)

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("ggbio", version = "3.8")

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("GenomeGraphs", version = "3.8")