User: Aurora

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Aurora10
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1 month ago
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9 months, 2 weeks ago
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Posts by Aurora

<prev • 27 results • page 1 of 3 • next >
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Comment: C: I can't install the pasilla package
... Thanks a lot ! ...
written 4 weeks ago by Aurora10
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I can't install the pasilla package
... Hi, I am trying to install the pasilla package by following the bioconductor website instructions : if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("pasilla", version = "3.8") But I have the following answer : Installing package int ...
pasilla biocmanager written 4 weeks ago by Aurora10 • updated 4 weeks ago by James W. MacDonald48k
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Comment: C: constructing a DESeqDataSet
... As far as I understood, DESeqDataSetFromTximport has the same purpose that DESeqDataSetFromMatrix but it can directly accept the output of a psedoaligner such as Salmon, producing directly the count matrix. With DESeqDataSetFromMatrix, you need to have a count matrix already prepared with genes as ...
written 6 months ago by Aurora10
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What does the relative-log expression normalization mean in the deseq2 wrapper function ?
... Good morning, I am trying to understand the relative log expression normalizat ion made by the DESEQ2 wrapper function. As far as I understood, It corresponds to the computing of scaling factor as described by Anders and Hubers (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11- ...
normalization deseq2 rle written 6 months ago by Aurora10 • updated 6 months ago by Michael Love20k
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Pathview results interpretation
... Good morning ! I have kegg pathway modification results thanks to pathview but I don't know how to interpret it. A rectangle corresponds to a gene ? A rectangle can be both green and red, what does it mean according to its regulation ? Why does the lengend values always go from -1 to 1 ? How can I ...
pathview interpretation written 6 months ago by Aurora10
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Comment: C: Troubles installing GO.db
... Thanks a lot ! I didn't notice that detail on this new computer. ...
written 6 months ago by Aurora10
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Troubles installing GO.db
... Good morning, I can"t install the GO.db package and I can't figure out how to do it. > biocLite("GO.db") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ‘GO.db’ installing the source package ‘GO.db’ trying URL 'h ...
go.db written 6 months ago by Aurora10 • updated 6 months ago by Martin Morgan ♦♦ 22k
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GAGE function and the same.dir option
... Good morning, I am trying to find perturbed pathway from expression date using a kegg gene set. In the GAGE paper (Luo et al., 2009), iit is recommanded to use the option same.dir=F on KEGG pathwayt is worthy to run gage with  to capture pathways perturbed towards both directions simultaneously. ...
gage gene set testing written 6 months ago by Aurora10 • updated 6 months ago by Luo Weijun1.4k
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Comment: C: Filtering Rna-seq counts
... Thanks a lot ! ...
written 6 months ago by Aurora10
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Filtering Rna-seq counts
... Hi, Filtering Rna-seq counts before performing differential expression analysis is generally recommanded. I wonder why is it recommanded?  What makes the analysis better that if no filtering was performed.?   Thank you for answers   ...
rna-seq filtering written 6 months ago by Aurora10 • updated 6 months ago by Gordon Smyth35k

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