User: ashley.doane

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ashley.doane20
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Posts by ashley.doane

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Epivisr namespace error
... Hi, With an updated Bioconductor, I get the following error loading the epivisr package.  Any suggestions for a possible fix would be great. library(epivizrStandalone) Loading required package: epivizr Error : .onLoad failed in loadNamespace() for 'epivizrStandalone', details: call: file(file, ...
epivizr written 19 months ago by ashley.doane20 • updated 19 months ago by Hector Corrada Bravo60
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Answer: A: Problem with biomart's listMarts function
... This seems to be not working again.  Please share if you know a solution! > library(biomaRt) > ensembl=useMart("ensembl") > ensembl=useMart("ensembl") ​Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Error: 1: Space required ...
written 19 months ago by ashley.doane20
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ChipQC report tables
... Is it possible to generate the html QC tables with a call to ChIPQCreport(), that does not include the commentary and interpretation narrative?   thanks Ashley   ...
chipq written 20 months ago by ashley.doane20 • updated 19 months ago by Thomas Carroll390
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motifbreakR VariantAnnotation namespace error on reading vcf file
... Hi I'm encountered the following error while reading a vcf file using the motifbreakR package.     vcf <- "/Users/asd2007/Tools/vcftools/examples/annotate-test.vcf" vars <- snps.from.file(file =vcf, search.genome = BSgenome.Hsapiens.UCSC.hg19, format = "vcf") Error: 'seqlevels<-' is ...
variantannotation motifbreakr written 2.1 years ago by ashley.doane20 • updated 2.1 years ago by Simon Coetzee40
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Answer: A: subset of samples from dba object in DiffBind
... Thanks Rory! ...
written 2.2 years ago by ashley.doane20
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subset of samples from dba object in DiffBind
...   Is it possible to create a new dba object based on a subset of the samples in a previous call to dba.count, or dba.analyze?   Basically, I would like analyze subsets of samples as seperate analyses, without recounting.  I'm analyzing atac-seq data, which is paired end and >50 million reads p ...
diffbind written 2.3 years ago by ashley.doane20
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How to annotate DESeq2 object with gene size to get FPKMs
... I'd like to annotate a DESeqDataSet with information on gene size, specifically populating mcols(dds)$basepairs, where dds is my DESeqDataSet.  The DESeqDataSet was created from HTSeq output, using the DESeqDataSetFromHTSeqCount function.           The reason for this is to pull out FPKMs, and ...
deseq2 fpkm written 2.4 years ago by ashley.doane20 • updated 2.4 years ago by Michael Love15k

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