User: Biologist

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Biologist130
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Posts by Biologist

<prev • 160 results • page 1 of 16 • next >
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Comment: C: genie3 for lncRNAs and mRNAs co-expression
... Instead of using only DE lncRNAs and DE mRNAs, you should input all the mRNAs and lncRNAs with some filtering like removing genes with low expression. You can check the `WGCNA` R package for Co-expression network analysis. ...
written 8 days ago by Biologist130
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Sure thanq. I will have a look. ...
written 10 days ago by Biologist130
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Thanks a ton @Jean-Karim Heriche Here 1000 genes expressed meaning, differentially expressed in tumor or just expressed? And 80 target genes of lncRNA X mean co-expressed genes or neighbouring genes? If it is co-expressed genes what should be the cutoff for selecting target genes? ...
written 10 days ago by Biologist130
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Here in the paper they say "each test was adjusted for the total number of lncRNAs, lncRNA targets, and gene set tested". I'm a bit confused how the contingency table should look for the fishers test in this type of analysis? If you don't mind Could you please tell with a small example mentioning ...
written 10 days ago by Biologist130
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Estimating gene set enrichment using Fishers exact test
... Hi, I'm working with lung cancer data and I'm interested in lncRNAs, I would like to identify lncRNAs that target key pathways. Recently, I read a paper which discusses about this type of analysis. Here is the paper [Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes ...
fisherstest rna-seq gsea lncrna written 10 days ago by Biologist130
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Comment: C: Survival analysis with gene expression
... Gud one Kevin. I have a question. On what basis Z-scale cutoff 1.0 is selected? BTW In this tutorial [http://r-addict.com/2016/11/21/Optimal-Cutpoint-maxstat.html] they have used `maxstat` (Maximally selected rank statistics) for the cutpoint to classify samples into high and low. ...
written 25 days ago by Biologist130
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Comment: C: Pick soft threshold for co-expression analysis and filtering step
... thanks a lot for the link Kevin ...
written 28 days ago by Biologist130
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Comment: C: Pick soft threshold for co-expression analysis and filtering step
... sure. thank you for the quick reply. ...
written 28 days ago by Biologist130
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Comment: C: Pick soft threshold for co-expression analysis and filtering step
... @Kevin Blighe In the second figure in my comments, I see 3 is above R square 0.8. So, I took softPower 3 when using log transformed values for WGCNA. Do you think this is right? Or should I use every time 6 or 7 as softPower? In most of the tutorials I see they are using 7 or 8. See in this tuto ...
written 28 days ago by Biologist130
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Comment: C: Pick soft threshold for co-expression analysis and filtering step
... Thank you very much for the link. ...
written 29 days ago by Biologist130

Latest awards to Biologist

Popular Question 18 days ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 28 days ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Student 10 weeks ago, asked a question with at least 3 up-votes. For Gene set enrichment analysis with edgeR output
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to make a color plot out of three columns from a dataframe in R?
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