User: lessismore

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lessismore650
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Posts by lessismore

<prev • 193 results • page 1 of 20 • next >
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associate GO ID with GO description
... Dear all, i have an enrichment output file displaying only GO IDs. Two questions: (1) Can somebody suggest a way to associate GO category description to the GO ID? Where do i retrieve such a file? Sorry for the maybe trivial question. (2) Would be also very much appreciated a tip on a tool to perf ...
go annotation written 11 days ago by lessismore650 • updated 11 days ago by Jean-Karim Heriche20k
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Comment: C: GO redundancy reduction
... Because i'd like to automate it and didn't find script to do it with REVIGO. ...
written 4 weeks ago by lessismore650
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GO redundancy reduction
... Dear all, i have a plain text file with a list of GO that were significant in my enrichment analysis and i would like to reduce its redundancy (just like REVIGO is doing). Could you please suggest a way to do this? Preferably an R package. Output should be another plain text file. Thanks in advanc ...
R enrichment written 5 weeks ago by lessismore650 • updated 4 weeks ago by Friederike4.6k
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Comment: C: Merge multiple list of IDs and summarize with a matrix
... Hi, i updated my inputs. Can you please be more clear on how to make this? Thanks! ...
written 5 weeks ago by lessismore650
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Merge multiple list of IDs and summarize with a matrix
... Dear all, i have 30 different lists of gene IDs partially overlapping and i want to create a matrix where i have on the rownames all of them and the columns should correspond to the lists and indicate if the gene ID was present or not there (1 or 0). here the inputs: several .txt files list1.txt ...
R written 5 weeks ago by lessismore650
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Comment: C: Alternative splicing analysis following kallisto?
... Hey! So far you are the only one using this approach. I didnt find a single paper mapping RNAseq data against rice transcriptome. Thats pretty curious ...
written 4 months ago by lessismore650
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Comment: C: Modifying Edge Weights in WGCNA
... > I do not know. Your educated guess is as good as mine. I would check > the overlap of the edges. Also, depending on how you constructed both > the GCN and the GRN, one may be more reliable than the other. That > would be the GRN, right? honestly i have no idea on my data cause unfortu ...
written 4 months ago by lessismore650
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Comment: C: Modifying Edge Weights in WGCNA
... 3 questions to anwer your question. Sorry in advance :) (1) My idea is to merge this information using GCN as the base (here the doubt/question: should i keep the edges in the GRN that are already present in my GCN or should i also add extra edges from GRN to GCN). In any case i will have a mixed ...
written 4 months ago by lessismore650
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Comment: C: Modifying Edge Weights in WGCNA
... Dear Kevin, didnt want to create another post for that. i comment here to your "Network analysis is network analysis". How do you see merging co-expression (e.g. with WGCNA correlation matrix) and gene regulatory networks (e.g. GENIE3), both filtered for a specific cutoff (first case correlation val ...
written 4 months ago by lessismore650
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Comment: C: how to get genes and their interactions from RNA-Seq data?
... Agree on the amazing review. Among all the GRN tools, GENIE3 still looks like the most promising one starting from expression data (and i would assume we all want to start from RNA-seq data nowadays). The next challenge in GRNs is to integrate experimentally validated data from multiple experimen ...
written 4 months ago by lessismore650

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