User: maya.kappil

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maya.kappil10
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Posts by maya.kappil

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GC content correction in salmon/deseq2 workflow for single-end RNAseq data
... Hello, My understanding is that it is possible to add a flag for GC content correction when quantifying reads using salmon but that this is really meant for paired-end data.  I'm wondering about what options there are to perform GC content correction on single-end RNA-seq data and to what extent it ...
edaseq deseq2 rna-seq salmon written 8 months ago by maya.kappil10 • updated 8 months ago by Michael Love24k
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WGCNA following salmon/DESeq2
... Hello! If I wanted to conduct WGCNA analysis following a salmon/DESeq2 workflow, would it be appropriate to use the matrix generated after applying the vst function on the dds object? Something akin to the following script: dds<- DESeqDataSetFromTximport(txi, coldata, design = ~ batch + Sex + B ...
deseq2 wgcna salmon written 8 months ago by maya.kappil10 • updated 8 months ago by Peter Langfelder2.1k

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