User: aishu.jp

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aishu.jp10
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Posts by aishu.jp

<prev • 6 results • page 1 of 1 • next >
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What is the ideal FDR and fold change cutoff to consider in a RNA-seq experiment and which one should be the priority for selecting the DEGs?
... I have a control vs treated time course RNA-seq plant data for which I am trying to construct gene coexpression network.I have used DESeq2 package to identify differential expression of genes. My aim is to identify genes that are exclusively differentially expressed in the time course experiment. ...
fdr deseq2 rna-seq deg fold change written 2.1 years ago by aishu.jp10
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Can I combine Blastp and interproscan .dat files in blast2go
... I have local Blastp results of 10000 protein sequences as xml files and I have separately completed interproscan analysis using the gene sequences of the same 10000 proteins in Blast2go. Both Blastp results and interproscan results are saved in .dat file format and .b2g file format individually usi ...
interproscan merge .dat file blast2go blastp written 2.2 years ago by aishu.jp10
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How to avoid duplicate edges between same node pair in a co-expression network
... I have a control vs treated RNA-seq plant data for which I am trying to construct gene co-expression network. The normalized count matrix of 6000 DEGs idenftifed are derived after rlog transformation was inputted to Cor() function and Pearson correlation was applied. The pair wise correlation anal ...
duplicate edges cytoscape rna-seq coexpression written 2.4 years ago by aishu.jp10 • updated 2.4 years ago by Kevin Blighe67k
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Can I combine Blastp and interproscan results for GO annotation in blast2go
... I have local Blastp results of 10000 protein sequences as xml files and I have completed interproscan analysis using the gene sequences of the same 10000 proteins in Blast2go. My query is Can I load the Blastp xml files and interproscan results in Blast2go for mapping and GO annotation in Blast2go ...
blast2go blastp interpro scan written 2.4 years ago by aishu.jp10
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Comment: A: How to manage self loops in gene coexpression network constructed from RNA-seq d
... Thank you sir for your help. Do any clustering techniques reduce the gene pairs and self looping ...
written 2.4 years ago by aishu.jp10
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How to manage self loops in gene coexpression network constructed from RNA-seq data
... I have a control vs treated RNA-seq plant data for which I am trying to construct gene coexpression network.I identifed a total of 6000 genes are significantly differential expressed genes using DESeq2 R package after applying FDR cutoff 0.05. The normalised count matrix of these 6000 genes derived ...
gene R cytoscape rna-seq written 2.5 years ago by aishu.jp10 • updated 2.4 years ago by zx87549.7k

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