User: anu014

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anu014180
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India
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5 years, 1 month ago
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Posts by anu014

<prev • 155 results • page 1 of 16 • next >
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Comment: C: Beta calculation & soft thresholding in WGCNA
... What is beta? The publication says it's calculated according to scale free Topology criteria. I don't understand this. ...
written 7 months ago by anu014180
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Comment: C: Beta calculation & soft thresholding in WGCNA
... Oh yes, I forgot to add. Below are the references - 1. For 1st, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559 2. Yes, thresholding in terms of gene network analysis. 1st we deduce Pearson coefficient between gene pairs and then select a threshold of Pearson coefficien ...
written 7 months ago by anu014180
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Beta calculation & soft thresholding in WGCNA
... Hello all, I wanted to know how beta is determined in order to calculate weighted network adjacency in WGCNA (Weighted correlation network analysis)? Also, if I'm not wrong thresholding means below a particular value the entities, here nodes, are removed. But in WGCNA number of nodes remain the sam ...
gene network next-gen tool langfelder written 7 months ago by anu014180
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Comment: C: ChIp-seq RNA-seq overlap
... Thanks a lot Devon for solving the problem! ...
written 20 months ago by anu014180
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Comment: C: ChIp-seq RNA-seq overlap
... Or I'll remove --perGroup option and create the graph like this : https://www.dropbox.com/s/gw0rc9jgsq09e69/trial1.pdf?dl=0 and then it can be compared? ...
written 20 months ago by anu014180
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Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon, I was wondering, will using either reference-point or scale-regions in computeMatrix for both chipseq n rnaseq data will work? ...
written 20 months ago by anu014180
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Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon, I took common rows between exon.bed and transcripts.bed and ran remaining commands : computeMatrixOperations cbind -m peaks_sorted_matrix1 rna_16hr_sorted_matrix1 -o output1.mat.gz plotProfile --matrixFile output1.mat.gz --outFileName trial.pdf --samplesLabel peaks rna_16hrs ...
written 20 months ago by anu014180
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Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon, But what if I have different/extra row in exon bed file (like this one : Chromosome 10072 10148)? Should I discard them? Won't I'll be losing data then? FYI, I am using exon file with RNA-seq data and transcript file with Chip-seq data. ...
written 21 months ago by anu014180
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Comment: C: ChIp-seq RNA-seq overlap
... Hi Devon , below are the commands and the bed files I used : computeMatrix scale-regions -S rna_16hr_sorted.bw -R m.sme_exons.bed --metagene -a 500 -b 500 --outFileName rna_16hr_sorted_matrix computeMatrix reference-point -S peak_sorted.bw -R m.sme_transcript.bed -a 500 -b 50 ...
written 21 months ago by anu014180
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Comment: A: Neoantigen prediction Tools
... Thanks a lot all! I'll try them and get back to you :) ...
written 21 months ago by anu014180

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