User: ZheFrench
ZheFrench • 10
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Posts by ZheFrench
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Comment:
C: ATACseqQC memory overflow issue
... Getting also process killed when reading huge bam file ~ 9G with readBamFile function.
...
written 14 days ago by
ZheFrench • 10
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... Trying to plot report ChIPQCreport with a sampleSheet containing 60 samples I get the following error.
Error: Dimensions exceed 50 inches (height and width are specified in 'in' not pixels). If you're sure you want a plot that big, use `limitsize = FALSE`.
CCPlot.png and CoverageHistogramPlot.pn ...
written 7 months ago by
ZheFrench • 10
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... Could you provide a more detailed example of code to use biomart object and extra columns to add for example GeneSymbol in the output of DEXSeqHTML ?
Not clear to me how you use mart and attributes parameters in DEXSeqHTML
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written 10 months ago by
ZheFrench • 10
• updated 10 months ago by
Alejandro Reyes • 1.6k
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... I'm treating RNA-SEQ with forward-reverse library.
In the doc part 2.5 you explained very well how to configure Strandedness using the python script and the -s reverse option..(as htseqcount...)
In part B of the tutorial, Preprocessing within R , it's not clear to me how you configure that only u ...
written 10 months ago by
ZheFrench • 10
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... I have a pair of chipseq. One is really bad. Mapping failed.
I was wondering if it's possible to analyse only one without the pair ?
Other question :
I tried to do the analyze with both of the samples even is one is not very good.
I did two different things : the first time I set the rule that ...
written 13 months ago by
ZheFrench • 10
• updated 13 months ago by
Rory Stark • 2.5k
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... By the way ,same question for Reactome ? and Kegg ? I think enrichKEGG use lastest remote version using use_internal_data=FALSE.
Is there a way to upgrade these anotations without upgrading R bioconductor. I'm stuck to R 3.3.1 and can't upgrage bioconductor withtout reinstalling a more recent vers ...
written 13 months ago by
ZheFrench • 10
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... DiffBind_2.2.12 . It's not 3D plot.I send you that.
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written 13 months ago by
ZheFrench • 10
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... I'm using clusterProfiler v3.2.14 for GO molecular function in human.
The background size is 16309.
Panther webtool give a size of 21002. Annotation Version and Release Date: GO Ontology database Released 2017-08-14
I was wondering which version of the GO database is use in ClusterProfiler. Why ...
written 13 months ago by
ZheFrench • 10
• updated 13 months ago by
Guido Hooiveld • 2.3k
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... Is there a way to grep the percentages PC1 and PC2 variance explained from dba.plotPCA in diffbind or chipQC ?
In my pca plot PC1 and PC2 numbers seem inversed . I'd like a way to recompute them from scratch (as asked here ) or to retrieve them to tcheck if they are wrongly sorted. Because from sev ...
written 13 months ago by
ZheFrench • 10
• updated 13 months ago by
Rory Stark • 2.5k
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... I found by myself, sorry to bother with this one, it was caused by a mistake in name of sample control inside my samplefiles.csv. Careless error :/ Sorry
Thanks!
...
written 15 months ago by
ZheFrench • 10
Latest awards to ZheFrench
Scholar
16 months ago,
created an answer that has been accepted.
For C: ChIPQC : ChIPQCreport(experiment) swap memory overload
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