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User: maya.kappil

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Posts by maya.kappil

<prev • 7 results • page 1 of 1 • next >
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Normalized transcript/exon counts for network analysis
... Hi! I would like to generate a cosplicing network similar to how it's described here (https://github.com/iancuo/cosplicingNetworks). My understanding is that I would need normalized exon/transcript counts prior to generating the network. For DEXSeq, I was planning to input the normalized exon cou ...
dexseq sva wgcna drimseq written 3 days ago by maya.kappil0 • updated 16 hours ago by gosia.nowicka30
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Isoform coexpression using WGCNA
... Hello, I have been working with transcript-level RNAseq data recently (mostly looking at differential transcript usage), and I was wondering if there is a preferred pipeline to look at coexpression of exon-level/transcript-level count data using WGCNA. I have seen a couple of methods described in ...
wgcna written 10 days ago by maya.kappil0
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Comment: C: WGCNA following salmon/DESeq2
... Thanks!  Ah, ok - that makes sense regarding the filtering.  In the code line for the filtering step, the 30 does refer to the sample size of my smallest comparison group.  Counts in low tens for at least this number of samples makes sense, and we do have roughly 50M reads/sample, so I can adjust th ...
written 12 weeks ago by maya.kappil0
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Comment: C: GC content correction in salmon/deseq2 workflow for single-end RNAseq data
... Great, thanks!   I do have the MultiQC output and will review them for the GC content curves. Right now, I'm doing DGE but would also like to look at differential transcript usage using something like the DRIMSeq package.  ...
written 12 weeks ago by maya.kappil0
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Comment: C: WGCNA following salmon/DESeq2
... Thanks for the quick response!   ...
written 12 weeks ago by maya.kappil0
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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 12 weeks ago by maya.kappil0 • updated 12 weeks ago by Michael Love22k
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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 12 weeks ago by maya.kappil0 • updated 12 weeks ago by Peter Langfelder1.7k

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