search for: genomicfeatures

...t that more than a few are required at any one time. >> Good practice is to load namespaces as required, using requireNamespace. > > Extensive package dependencies in Bioconductor make it pretty easy to end up with dozen of packages attached or loaded. For instance > > library(GenomicFeatures) > library(DESeq2) > > > length(loadedNamespaces()) > [1] 63 > > length(getLoadedDLLs()) > [1] 41 > > Qin's use case is a shiny app, presumably trying to provide relatively comprehensive access to a particular domain. Even if the app were to load / requireNamesp...

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

On 04/05/2016 08:44, Martin Maechler wrote: >>>>>> Qin Zhu <qinzhu at outlook.com> >>>>>> on Mon, 2 May 2016 16:19:44 -0400 writes: > > > Hi, > > I?m working on a Shiny app for statistical analysis. I ran into this "maximal number of DLLs reached" issue recently because my app requires importing many other packages.

...packages, and I doubt that more than a few are required at any one time. > Good practice is to load namespaces as required, using requireNamespace. Extensive package dependencies in Bioconductor make it pretty easy to end up with dozen of packages attached or loaded. For instance library(GenomicFeatures) library(DESeq2) > length(loadedNamespaces()) [1] 63 > length(getLoadedDLLs()) [1] 41 Qin's use case is a shiny app, presumably trying to provide relatively comprehensive access to a particular domain. Even if the app were to load / requireNamespace() (this requires considerable...

...any one time. >>> Good practice is to load namespaces as required, using requireNamespace. >> >> Extensive package dependencies in Bioconductor make it pretty easy to end up with dozen of packages attached or loaded. For instance >> >> library(GenomicFeatures) >> library(DESeq2) >> >> > length(loadedNamespaces()) >> [1] 63 >> > length(getLoadedDLLs()) >> [1] 41 >> >> Qin's use case is a shiny app, presumably trying to provide relatively comprehensive access to a...

...trange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome") library("Biostrings") 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 locall...

...R-fontBitstreamVera * R-fontLiberation * R-forcats * R-foreach * R-formatR * R-fortunes * R-fs * R-fts * R-futile.logger * R-futile.options * R-future * R-gamlss.dist * R-gapminder * R-gdata * R-gdtools * R-gee * R-geepack * R-generics * R-GenomeInfoDb * R-GenomeInfoDbData * R-GenomicAlignments * R-GenomicFeatures * R-GenomicRanges * R-getPass * R-ggplot2 * R-ggplot2movies * R-gh * R-git2r * R-globals * R-glue * R-gmailr * R-gmp * R-gplots * R-gsl * R-gss * R-gtable * R-gtools * R-haven * R-here * R-hexbin * R-hgu133acdf * R-hgu95av2cdf * R-hgu95av2probe * R-highlight * R-highr * R-hms * R-htmltools * R-html...