knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(misha)
misha
database from UCSCIn order to create a misha database for hg19 genome, run the following commands (assuming "hg19" is your new data base path):
ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19" gdb.create( "hg19", paste(ftp, "chromosomes", paste0("chr", c(1:22, "X", "Y", "M"), ".fa.gz"), sep = "/"), paste(ftp, "database/knownGene.txt.gz", sep = "/"), paste(ftp, "database/kgXref.txt.gz", sep = "/"), c( "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol", "refseq", "protAcc", "description", "rfamAcc", "tRnaName" ) ) gdb.init("hg19")
In order to create a misha database for hg38 genome, run the following commands (assuming "hg38" is your new data base path):
ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38" gdb.create( "hg38", paste(ftp, "chromosomes", paste0("chr", c(1:22, "X", "Y", "M"), ".fa.gz"), sep = "/"), paste(ftp, "database/knownGene.txt.gz", sep = "/"), paste(ftp, "database/kgXref.txt.gz", sep = "/"), c( "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol", "refseq", "protAcc", "description", "rfamAcc", "tRnaName" ) ) gdb.init("hg19")
In order to create a misha database for mm9 genome, run the following commands (assuming "mm9" is your new data base path):
ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9" gdb.create( "mm9", paste(ftp, "chromosomes", paste0("chr", c(1:19, "X", "Y", "M"), ".fa.gz"), sep = "/"), paste(ftp, "database/knownGene.txt.gz", sep = "/"), paste(ftp, "database/kgXref.txt.gz", sep = "/"), c( "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol", "refseq", "protAcc", "description" ) ) gdb.init("mm9")
In order to create a misha database for mm10 genome, run the following commands (assuming "mm10" is your new data base path):
ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10" gdb.create( "mm10", paste(ftp, "chromosomes", paste0("chr", c(1:19, "X", "Y", "M"), ".fa.gz"), sep = "/"), paste(ftp, "database/knownGene.txt.gz", sep = "/"), paste(ftp, "database/kgXref.txt.gz", sep = "/"), c( "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol", "refseq", "protAcc", "description", "rfamAcc", "tRnaName" ) ) gdb.init("mm10")
In order to create a misha database for mm39 genome, run the following commands (assuming "mm39" is your new data base path):
ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39" gdb.create( "mm39", paste(ftp, "chromosomes", paste0("chr", c(1:19, "X", "Y", "M"), ".fa.gz"), sep = "/"), paste(ftp, "database/knownGene.txt.gz", sep = "/"), paste(ftp, "database/kgXref.txt.gz", sep = "/"), c( "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol", "refseq", "protAcc", "description", "rfamAcc", "tRnaName" ) ) gdb.init("mm39")
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