User: maya.kappil

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maya.kappil20
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Posts by maya.kappil

<prev • 11 results • page 1 of 2 • next >
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Module preservation using adjacency matrix (WGCNA)
... Hi, I'm trying out the CoSplicEx pipeline that feeds into WGCNA (https://github.com/iancuo/cosplicingNetworks). To test module preservation, the script loads adjacency matrices, but I get an error regarding the rownames. Below, I recreate the error using some random matrices. Any insight into wh ...
wgcna written 15 days ago by maya.kappil20 • updated 15 days ago by Peter Langfelder1.9k
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Comment: C: Parallel computing for IsoformSwitchAnalyzeR
... Hmm... I have somewhat more transcripts using the default preFilter setting (~80K). And, the calculated time to run DEXSeq seemed really large (17763754)... So far, I've tried running it for 15hrs (both correcting for a confounding variable and without correction) and they did not go to completion. ...
written 10 weeks ago by maya.kappil20
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Parallel computing for IsoformSwitchAnalyzeR
... Hello! I am interested to run the IsoformSwitchAnalyzeR package to assess differential transcript usage and related downstream analysis. However, I have a large set of RNAseq samples (200) - for the native DRIMSeq and DEXSeq packages, it is possible to add a command to indicate the number of cores ...
isoformswitchanalyzer written 10 weeks ago by maya.kappil20 • updated 10 weeks ago by k.vitting.seerup90
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Comment: C: Normalized transcript/exon counts for network analysis
... Ah, ok - that makes sense! Thanks!! ...
written 11 weeks ago by maya.kappil20
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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 12 weeks ago by maya.kappil20 • updated 12 weeks ago by Gosia Nowicka40
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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 3 months ago by maya.kappil20
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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 5 months ago by maya.kappil20
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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 5 months ago by maya.kappil20
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Comment: C: WGCNA following salmon/DESeq2
... Thanks for the quick response!   ...
written 5 months ago by maya.kappil20
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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 5 months ago by maya.kappil20 • updated 5 months ago by Michael Love23k

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