User: IrK

gravatar for IrK
IrK20
Reputation:
20
Status:
New User
Location:
Australia
Last seen:
2 months, 2 weeks ago
Joined:
2 years, 9 months ago
Email:
i*******@gmail.com

Posts by IrK

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Gene-based clustering of RNA-seq data
... Thank you so much for detailed clarification, Kevin, appreciate it! ...
written 3 months ago by IrK20
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Gene-based clustering of RNA-seq data
... Hey everyone, I am trying to understand the gene-based clustering, and what strategy can be applied to see what genes fall into the same cluster based on their expression profile. I have RNA-seq data that has been analyzed with DESeq2 package for differentially expressed genes. I selected rlog n ...
clustering gene-based clustering deseq2 rna-seq written 3 months ago by IrK20 • updated 3 months ago by Kevin Blighe28k
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Cogena framework for RNA-seq / minimum sample size
... Dear Zhilong Jia, I am wondering if Cogena framework is a statistically appropriate method for co-expressed gene set enrichment analysis of RNA-seq dataset, considering that input dataset (gene counts) is appropriately normalized? What is the minimum samples number that can be used? Would 3KOs v ...
cogena tool drug repositioning pathway written 3 months ago by IrK20
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Comment: A: Differential lncRNA-mRNA co-expression
... Could you please you share the link you wanted to post ? Or kind of approach have you undertaken? Thanks ...
written 4 months ago by IrK20
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Comment: C: Gene Co-expression analysis with less number of replicates
... I have 3KOs vs 3WTs (biological replicates), WTs have to be excluded from this kind of analysis that leaves only three KO samples. So I conclude it's not possible to build coexpression network in my case as well. Very sad!!! Sounded like very interesting kind of analysis to learn. Martombo, thank ...
written 4 months ago by IrK20
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Comment: A: Gene Co-expression analysis with less number of replicates
... Hi Amol, Did you find the answer to your question? I also have three replicates and I'd like to do gene coexpression analysis, and I can't find alternative to WGCNA. Thanks ...
written 4 months ago by IrK20
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Comment: C: Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
... To be honest, I checked that NAs are absent in gene IDs vector, but forgot that numeric values also can be represented as NAs in DESeqoutput$padj vector. ...
written 12 months ago by IrK20
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Answer: A: Goseq: Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
... I had the same error message and in my case it a binary vector had NAs, so basically: > genes = as.integer(DESeqoutput$padj <= 0.05 & > !is.na(DESeqoutput$padj)) # Give all values less than 0.05 and no NAs However, when I call for nullp() I get following warning: Can't find ...
written 12 months ago by IrK20
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Comment: C: How realible samtools/ bam-readcount /igvtools /pysamstats for finding deletions
... I just would like to summarize base-calls of aligned reads to each position. So it means that we get kind of base-call summary from options (2), (3), (4), can you trust this statistics? ...
written 12 months ago by IrK20
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How realible samtools/ bam-readcount /igvtools /pysamstats for finding deletions/insertions?
... Dear Biostarts users, This is my first time when I have to use variant-calling software/packages, so I would like to ask the opinion on mentioned below tools. How reliable are results produced by them? My goal is to find appearance of A,C,T,G or DEL, INS at each base across chr1 (Not a whole gen ...
igvtools bam-readcounts samtools pysamstats written 12 months ago by IrK20 • updated 11 months ago by Biostar ♦♦ 20

Latest awards to IrK

Popular Question 12 months ago, created a question with more than 1,000 views. For How to find if a string contains non overlapping block of repeated units? Python
Popular Question 18 months ago, created a question with more than 1,000 views. For How to find if a string contains non overlapping block of repeated units? Python
Popular Question 18 months ago, created a question with more than 1,000 views. For GSEA /enrichment plot with heat map
Popular Question 18 months ago, created a question with more than 1,000 views. For TMM normalization for RNA seq data with three replicates (2 samples)

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