User: lessismore

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lessismore600
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Posts by lessismore

<prev • 188 results • page 1 of 19 • next >
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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 9 hours ago by lessismore600
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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 17 days ago by lessismore600
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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 17 days ago by lessismore600
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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 17 days ago by lessismore600
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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 19 days ago by lessismore600
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network visualization (multiple data source integration)
... Dear all, i am dealing with network visualization and i would like to know if you feel like recommending tools for network visualization integrating multiple sources of data. For that i mean also including scores/colours/thickness features for edges based on multiple "evidences" on already computed ...
networks network visualization written 24 days ago by lessismore600 • updated 3 days ago by Biostar ♦♦ 20
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Comment: C: How to eliminate batch effect using removeBatchEffect function for tissue expres
... i'd rather suggest BatchQC for batch effect removal + visualization + statistics https://bioconductor.org/packages/release/bioc/html/BatchQC.html ...
written 3 months ago by lessismore600
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Comment: C: cannot replicate the pheatmap scale function
... Hey igor, it's the same clustering in my case because i am comparing manually scaled > pheatmap function with `scale=none` VS pheatmap scaled with `scale=rows` ...
written 4 months ago by lessismore600
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Comment: C: cannot replicate the pheatmap scale function
... That's the only explanation! Thanks ...
written 4 months ago by lessismore600
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Comment: C: Network enrichment analysis
... maybe the WGCNA paper itself will be good > https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559 ...
written 4 months ago by lessismore600

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