search for: txdb

...?, ?hgu95av2probe?, ?hgu95av2cdf?, ?SNPlocs.Hsapiens.dbSNP.20100427?, ?SNPlocs.Hsapiens.dbSNP.20101109?, ?SNPlocs.Hsapiens.dbSNP.20110815?, ?SNPlocs.Hsapiens.dbSNP141.GRCh38?, ?XtraSNPlocs.Hsapiens.dbSNP141.GRCh38?, ?org.Sc.sgd.db?, ?org.Mm.eg.db?, ?org.At.tair.db?, ?hom.Hs.inp.db?, ?GO.db?, ?TxDb.Hsapiens.UCSC.hg18.knownGene?, ?TxDb.Hsapiens.UCSC.hg19.knownGene?, ?TxDb.Hsapiens.UCSC.hg38.knownGene?, ?TxDb.Mmusculus.UCSC.mm9.knownGene?, ?TxDb.Mmusculus.UCSC.mm10.knownGene?, ?TxDb.Dmelanogaster.UCSC. [... truncated] 2: In install.packages(pkgs = doing, lib = lib, ...) : installation o...

...") library("BSgenome.Hsapiens.UCSC.hg19") library("biomaRt") library("GenomicFeatures") #extract the alignments which match real genes #(add this onto stefans script … req to buid the gr object using the regions from the BSgenome alignment of the 100bp seqs.) txdb <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") ## do once locally & save #query.plus <- DNAString("DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD") # 100bp C free sequence query.p...

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

...s_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] profvis_0.3.3 bindrcpp_0.2 [3] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.4.1 [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.28.4 [7] AnnotationDbi_1.38.2 Biobase_2.36.2 [9] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 [11] IRanges_2.10.2 S4Vectors_0.14.3 [13] BiocGenerics_0.22.0 epian...