User: krwyaong.ju

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Posts by krwyaong.ju

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summarizeOverlaps 'sequences have incompatible seqlengths' errors
... I follow the tutorial; RNA-Seq differential expression work flow using DESeq2 (http://www.sthda.com/english/wiki/rna-seq-differential-expression-work-flow-using-deseq2). I've got stuck below; Could you figure it out? > library( "GenomicAlignments" ) > se <- summarizeOverlaps( exonsByGene ...
deseq2 written 10 months ago by krwyaong.ju0 • updated 10 months ago by Martin Morgan ♦♦ 23k
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there is no "tx2gene.gencode.v27.csv" in tximportData
... as installed tximportData, there was no "tx2gene.gencode.v27.csv". below is the shell for installation; > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent ...
tximport written 10 months ago by krwyaong.ju0 • updated 10 months ago by Michael Love22k
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installation of "GenomicFeatures"
... installation of "GenomicFeatures" failed; pls say how to figure it out? > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help > biocLite("GenomicFeatures") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstalle ...
genomicfeatures written 11 months ago by krwyaong.ju0 • updated 11 months ago by James W. MacDonald49k
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Comment: A: use deseq2 in asthma
... I 've done. seems no need of "here", I gave the correct path without writing "here" in your scripts. another question; how to install "GenomeFeatures". many tries but failed. how to do? ...
written 11 months ago by krwyaong.ju0
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Comment: A: use deseq2 in asthma
... > list.files("../data/quants/") character(0) > list.files("/home/jkr/asthma/data/quants/")  [1] "SRR1565926" "SRR1565927" "SRR1565928" "SRR1565929" "SRR1565930"  [6] "SRR1565931" "SRR1565932" "SRR1565933" "SRR1565934" "SRR1565935" [11] "SRR1565936" "SRR1565937" "SRR1565938" "SRR1565939" "SRR15 ...
written 11 months ago by krwyaong.ju0
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Tutorial: use deseq2 in asthma
... Dear Michael Love, I am interested in your github; https://github.com/mikelove/asthma/blob/master/scripts/asthma.Rmd I installed all packages as your guidelines (https://angus.readthedocs.io/en/2017/deseq2-asthma.html) now I am running your scripts on Ubuntu16.04. list.files("../data/quants/") . ...
deseq2 tutorial written 11 months ago by krwyaong.ju0

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