User: maya.kappil

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maya.kappil10
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Posts by maya.kappil

<prev • 13 results • page 1 of 2 • next >
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Data input for aracne2regulon function in viper package
... Hello, I have run the viper workflow using the test data-set, but I'm having trouble using my own data using a regulatory network generated with ARACNe-AP. Unfortunately, ARACNe-AP no longer seems to output adj files as used in the viper vignette. Instead I have a text file that represents a conso ...
viper written 8 weeks ago by maya.kappil10
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gwascat: error regarding mismatched genome builds when using makeCurrentGwascat()
... Hello, I was able to match some disease traits to SNPs I'm interested in based on the NHGRI GWAS catalog website, and I'm now interested to use the gwascat R package to plot my findings with these GWAS hits. These GWAS hits were published relatively recently, so I'm not able to utilize the preload ...
gwascat written 3 months ago by maya.kappil10
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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 5 months ago by maya.kappil10 • updated 5 months ago by Peter Langfelder2.2k
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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 7 months ago by maya.kappil10
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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 7 months ago by maya.kappil10 • updated 7 months ago by k.vitting.seerup100
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Comment: C: Normalized transcript/exon counts for network analysis
... Ah, ok - that makes sense! Thanks!! ...
written 7 months ago by maya.kappil10
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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 8 months ago by maya.kappil10 • updated 8 months 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 8 months ago by maya.kappil10
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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 10 months ago by maya.kappil10
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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 10 months ago by maya.kappil10

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