I tried to install and use BSgenome, but I have problem in reading from the library. Do I need other arrangement to assess to the library? Please help: source("http://www.bioconductor.org/biocLite.R") biocLite("BSgenome") require(BSgenome) > available.genomes() BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). [1] "BSgenome.Amellifera.BeeBase.assembly4" [2] "BSgenome.Amellifera.UCSC.apiMel2" [3] "BSgenome.Athaliana.TAIR.01222004" [4] "BSgenome.Athaliana.TAIR.04232008" [5] "BSgenome.Athaliana.TAIR.TAIR9" [6] "BSgenome.Btaurus.UCSC.bosTau3" [7] "BSgenome.Btaurus.UCSC.bosTau4" [8] "BSgenome.Celegans.UCSC.ce2" [9] "BSgenome.Celegans.UCSC.ce6" [10] "BSgenome.Cfamiliaris.UCSC.canFam2" [11] "BSgenome.Dmelanogaster.UCSC.dm2" [12] "BSgenome.Dmelanogaster.UCSC.dm3" [13] "BSgenome.Drerio.UCSC.danRer5" [14] "BSgenome.Drerio.UCSC.danRer6" [15] "BSgenome.Ecoli.NCBI.20080805" [16] "BSgenome.Ggallus.UCSC.galGal3" [17] "BSgenome.Hsapiens.UCSC.hg17" [18] "BSgenome.Hsapiens.UCSC.hg18" [19] "BSgenome.Hsapiens.UCSC.hg19" [20] "BSgenome.Mmusculus.UCSC.mm8" [21] "BSgenome.Mmusculus.UCSC.mm9" [22] "BSgenome.Ptroglodytes.UCSC.panTro2" [23] "BSgenome.Rnorvegicus.UCSC.rn4" [24] "BSgenome.Scerevisiae.UCSC.sacCer1" [25] "BSgenome.Scerevisiae.UCSC.sacCer2" > library(BSgenome.Athaliana.TAIR.TAIR9) Error in library(BSgenome.Athaliana.TAIR.TAIR9) : there is no package called 'BSgenome.Athaliana.TAIR.TAIR9' > library("BSgenome.Athaliana.TAIR.TAIR9") Error in library("BSgenome.Athaliana.TAIR.TAIR9") : there is no package called 'BSgenome.Athaliana.TAIR.TAIR9' > library("BSgenome.Hsapiens.UCSC.hg17") Error in library("BSgenome.Hsapiens.UCSC.hg17") : there is no package called 'BSgenome.Hsapiens.UCSC.hg17' Am I missing some dependencies? Please help: -- Ram H [[alternative HTML version deleted]]

On 09/17/2011 01:38 PM, Ram H. Sharma wrote: > I tried to install and use BSgenome, but I have problem in reading from the > library. Do I need other arrangement to assess to the library? > Please help: > > source("http://www.bioconductor.org/biocLite.R") > biocLite("BSgenome") > require(BSgenome) > >> available.genomes() Hi Ram -- Individual genomes need to be installed. See installed.genomes() and source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Athaliana.TAIR.TAIR9") Martin > > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). > [1] "BSgenome.Amellifera.BeeBase.assembly4" > [2] "BSgenome.Amellifera.UCSC.apiMel2" > [3] "BSgenome.Athaliana.TAIR.01222004" > [4] "BSgenome.Athaliana.TAIR.04232008" > [5] "BSgenome.Athaliana.TAIR.TAIR9" > [6] "BSgenome.Btaurus.UCSC.bosTau3" > [7] "BSgenome.Btaurus.UCSC.bosTau4" > [8] "BSgenome.Celegans.UCSC.ce2" > [9] "BSgenome.Celegans.UCSC.ce6" > [10] "BSgenome.Cfamiliaris.UCSC.canFam2" > [11] "BSgenome.Dmelanogaster.UCSC.dm2" > [12] "BSgenome.Dmelanogaster.UCSC.dm3" > [13] "BSgenome.Drerio.UCSC.danRer5" > [14] "BSgenome.Drerio.UCSC.danRer6" > [15] "BSgenome.Ecoli.NCBI.20080805" > [16] "BSgenome.Ggallus.UCSC.galGal3" > [17] "BSgenome.Hsapiens.UCSC.hg17" > [18] "BSgenome.Hsapiens.UCSC.hg18" > [19] "BSgenome.Hsapiens.UCSC.hg19" > [20] "BSgenome.Mmusculus.UCSC.mm8" > [21] "BSgenome.Mmusculus.UCSC.mm9" > [22] "BSgenome.Ptroglodytes.UCSC.panTro2" > [23] "BSgenome.Rnorvegicus.UCSC.rn4" > [24] "BSgenome.Scerevisiae.UCSC.sacCer1" > [25] "BSgenome.Scerevisiae.UCSC.sacCer2" > >> library(BSgenome.Athaliana.TAIR.TAIR9) > Error in library(BSgenome.Athaliana.TAIR.TAIR9) : > there is no package called 'BSgenome.Athaliana.TAIR.TAIR9' > >> library("BSgenome.Athaliana.TAIR.TAIR9") > Error in library("BSgenome.Athaliana.TAIR.TAIR9") : > there is no package called 'BSgenome.Athaliana.TAIR.TAIR9' >> library("BSgenome.Hsapiens.UCSC.hg17") > Error in library("BSgenome.Hsapiens.UCSC.hg17") : > there is no package called 'BSgenome.Hsapiens.UCSC.hg17' > > Am I missing some dependencies? Please help: > > -- > > Ram H > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

On Sat, Sep 17, 2011 at 4:38 PM, Ram H. Sharma <sharma.ram.h at="" gmail.com=""> wrote: > I tried to install and use BSgenome, but I have problem in reading from the > library. Do I need other arrangement to assess to the library? > Please help: > > ?source("http://www.bioconductor.org/biocLite.R") > ? ?biocLite("BSgenome") > ? ?require(BSgenome) > >> ?available.genomes() > > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). > ?[1] "BSgenome.Amellifera.BeeBase.assembly4" > ?[2] "BSgenome.Amellifera.UCSC.apiMel2" > ?[3] "BSgenome.Athaliana.TAIR.01222004" > ?[4] "BSgenome.Athaliana.TAIR.04232008" > ?[5] "BSgenome.Athaliana.TAIR.TAIR9" > ?[6] "BSgenome.Btaurus.UCSC.bosTau3" > ?[7] "BSgenome.Btaurus.UCSC.bosTau4" > ?[8] "BSgenome.Celegans.UCSC.ce2" > ?[9] "BSgenome.Celegans.UCSC.ce6" > [10] "BSgenome.Cfamiliaris.UCSC.canFam2" > [11] "BSgenome.Dmelanogaster.UCSC.dm2" > [12] "BSgenome.Dmelanogaster.UCSC.dm3" > [13] "BSgenome.Drerio.UCSC.danRer5" > [14] "BSgenome.Drerio.UCSC.danRer6" > [15] "BSgenome.Ecoli.NCBI.20080805" > [16] "BSgenome.Ggallus.UCSC.galGal3" > [17] "BSgenome.Hsapiens.UCSC.hg17" > [18] "BSgenome.Hsapiens.UCSC.hg18" > [19] "BSgenome.Hsapiens.UCSC.hg19" > [20] "BSgenome.Mmusculus.UCSC.mm8" > [21] "BSgenome.Mmusculus.UCSC.mm9" > [22] "BSgenome.Ptroglodytes.UCSC.panTro2" > [23] "BSgenome.Rnorvegicus.UCSC.rn4" > [24] "BSgenome.Scerevisiae.UCSC.sacCer1" > [25] "BSgenome.Scerevisiae.UCSC.sacCer2" > >> library(BSgenome.Athaliana.TAIR.TAIR9) > Error in library(BSgenome.Athaliana.TAIR.TAIR9) : > ?there is no package called 'BSgenome.Athaliana.TAIR.TAIR9' > >> library("BSgenome.Athaliana.TAIR.TAIR9") > Error in library("BSgenome.Athaliana.TAIR.TAIR9") : > ?there is no package called 'BSgenome.Athaliana.TAIR.TAIR9' >> ?library("BSgenome.Hsapiens.UCSC.hg17") > Error in library("BSgenome.Hsapiens.UCSC.hg17") : > ?there is no package called 'BSgenome.Hsapiens.UCSC.hg17' > > Am I missing some dependencies? Please help: Hi, Ram. You need to install the package first: biocLite('BSgenome.Athaliana.TAIR.TAIR9') Then: library('BSgenome.Athaliana.TAIR.TAIR9') Sean