User: warrena

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warrena0
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Posts by warrena

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getting mouse gene ids from makeTxDbFromUCSC()
... I am trying to get mm10 gene annotations with gene names. I have tried the following: ncbiRefSeq = makeTxDbFromUCSC(genome="mm10", tablename="ncbiRefSeq") geneid = makeTxDbFromUCSC(genome="mm10", tablename="geneid") knownGene = makeTxDbFromUCSC(genome="mm10", tablename="knownGene") In the first ...
genomicfeatures maketxdbfromucsc written 7 weeks ago by warrena0 • updated 7 weeks ago by shepherl ♦♦ 730
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Comment: C: error with detectTranscripts
... Thanks, Anusha. This worked. I'll add that for users of R 3.4.4 I had to call keepStandardChromosomes() with pruning.mode="coarse". Here is the code: require(groHMM) library(IRanges) library(GenomicRanges) library(Rsamtools) library(GenomicAlignments) data <- readGAlignments("poolA_index1_samp ...
written 10 weeks ago by warrena0
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error with detectTranscripts
... Greetings, I am attempting to use detectTranscripts() from groHMM using bams from a PRO-seq experiment. I am getting the following error: Error in Fp[[i]] + 1 : non-numeric argument to binary operator In addition: Warning messages: 1: In mclapply(readsList, function(x) { :   all scheduled cores en ...
grohmm written 10 weeks ago by warrena0 • updated 10 weeks ago by lee.kraus0
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non-integer counts in DESeq2
... I have PRO-seq data with the following conditions: untreated (time 0), vehicle, and treatment (3 replicates each, 4 time points for each vehicle/treatment combination). I would like to evaluate treatment effects as a function of time. I have done the following: 1. Divided the reads in each conditio ...
deseq2 differential gene expression written 3 months ago by warrena0 • updated 3 months ago by Michael Love19k

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