User: anusha.nagari

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UT SOUTHWESTERN MEDICAL CENTER
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Posts by anusha.nagari

<prev • 6 results • page 1 of 1 • next >
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Comment: C: How to export TSV groHMM file using called transcripts rather than known genes
... Please let us know if you run into any issues using the functions of our package. Unfortunately, we cannot help you with questions that are not directly related to troubleshooting of the package. Thanks for your understanding.  ...
written 5 days ago by anusha.nagari30
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Answer: A: How do I get groseq signal for each gene from groSeq in groHMM
... Hello, You can do that using the following extension to section 3.8 in the tutorial: d <- calcNormFactors(d) d_rpkm <- data.frame(rpkm(d,width(kgChr7),normalized.lib.sizes=TRUE)) gene_rpkm <- data.frame(kgChr7,kgLimit, d_rpkm) head(gene_rpkm)     ...
written 13 days ago by anusha.nagari30
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Comment: C: error when I use groHMM on data outside of the tutorial
... Hello, Can you try including just the standard chromosomes and then execute the writeWiggle step.  gr <- keepStandardChromosomes(SRR5364056) or if you are using  R 3.4.4 gr <- keepStandardChromosomes(SRR5364056, pruning.mode="coarse")       ...
written 4 weeks ago by anusha.nagari30
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Comment: C: error with detectTranscripts
... Hello! Removing the random chr annotations (chrUn_gl0000230, chr9_gl000198_random) from your bam file should take of that error with the current version of groHMM package. Please try:  Sall_stdchr <- keepStandardChromosomes(Sall) hmmResult <- detectTranscripts(Sall_stdchr, LtProbB=-200, UTS= ...
written 3 months ago by anusha.nagari30
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Help with R CMD check NOTEs
... Hello,   I am getting the following NOTES at R CMD check step:   NOTE1: * checking package dependencies ... NOTE Depends: includes the non-default packages:   ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’   ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ Adding so many packages to the sea ...
r cmd check written 12 months ago by anusha.nagari30 • updated 12 months ago by Martin Morgan ♦♦ 22k
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Comment: C: Error in normalizeDoubleBracketSubscript()
... Thanks for the reply. Here is the code: require(groHMM) library(IRanges) library(GenomicRanges) windowAnalysis <- function(reads, strand="*", windowSize=stepSize, stepSize=windowSize, chrom=NULL, limitPCRDups=FALSE,mc.cores=1, ...) { if (!(windowSize > 0 & (windowSize <= max( ...
written 3.0 years ago by anusha.nagari30

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