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User: Reza

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Reza • 0
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Posts by Reza

<prev • 17 results • page 1 of 2 • next >
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Identification of lncRNA target genes
... Dear all, I have RNA seq data from different tissues of one plant with the reference genome. I am trying to find out target genes of lncRNAs as cis-acting target genes. How can I identify and separate the target genes within 100 kb upstream or downstream of lncRNAs? Are there any codes or packages ...
plant target lncrna rna-seq sequencing written 3 days ago by Reza • 0
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Target genes of lncRNAs
... Dear all, I have RNA seq data from different tissues of one plant with the reference genome. I am trying to find out target genes of lncRNAs as cis-acting target genes. How can I identify and separate the target genes within 100 kb upstream or downstream of lncRNAs? Are there any codes or packages ...
bioinformatics lncrnas cufflinks rna-seq written 9 days ago by Reza • 0
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Comment: C: Is it possible to detect lncRNA in a de novo assembled genome?
... Hi Wouter, I assembled the raw reads into transcripts (contigs) and used it as reference genome. ...
written 18 months ago by Reza • 0
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Comment: C: Is it possible to detect lncRNA in a de novo assembled genome?
... Thank you for your answer. ...
written 18 months ago by Reza • 0
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Is it possible to detect lncRNA in a de novo assembled genome?
... Hello everybody, I have RNAseq data from species that the genome reference is not available and I'd like detect lncRNA. Do you think that this is possible? Thanks, ...
genome assembly rna-seq written 18 months ago by Reza • 0 • updated 16 months ago by grant.hovhannisyan • 2.0k
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How to prepare trait data file of categorical trait with more than two levels for WGCNA?
... Hi everyone, I want to do WGCNA and estimate the correlation of modules with clinical traits. The clinical information includes nominal variable with more than two levels (not binary). How I can design and create clinicaltrait.txt file? I have attached a screenshot of the trait file, please have a ...
R rna-seq wgcna written 19 months ago by Reza • 0 • updated 19 months ago by Kevin Blighe ♦ 69k
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recursive SVM classification using MetaboAnalyst
... Hi everyone, I performed recursive SVM classification for my data by “***RSVM.Anal(mSet, 10)***” and “***PlotRSVM.Classification***” functions of **MetaboAnalystR** package and error rates of different subsets were determined such as this figure ![enter image description here][1]. Is there a way ...
R svm metaboanalystr written 2.0 years ago by Reza • 0 • updated 22 months ago by Biostar ♦♦ 20
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How to prepare input data for DiffCoEx
... Hi everyone, I want to identify differentially co-expressed gene modules for two different species by **DiffCoEx** according to [this][1] article. I have used RMA method to normalize data for two datasets. How to prepare and organize data for WGCNA? Thanks [1]: https://journals.plos.org/plo ...
wgcna transcriptome R written 2.1 years ago by Reza • 0
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error in running maser 0.99.16
... Hi everyone, I'm using rMATS for alternative splicing analysis. I want to visualize the output by maser 0.99.16 but encountered the following error. Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 4462: range cannot be determined from the ...
R alternative splicing written 2.4 years ago by Reza • 0 • updated 2.4 years ago by _r_am ♦ 32k
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Getting error in running rMATS
... Hi everyone, I'm trying to run rMATS to get alternative splicing but encountered some errors. Errors found: ========== Done processing each gene from dictionary to compile AS events Found 14962 exon skipping events Found 1100 exon MX events Found 28836 alt SS events There ...
software error rmats rna-seq alternative splicing written 2.4 years ago by Reza • 0

Latest awards to Reza

Popular Question 14 months ago, created a question with more than 1,000 views. For Getting error in running rMATS
Popular Question 14 months ago, created a question with more than 1,000 views. For gene expression correlation, FPKM, WGCNA
Popular Question 14 months ago, created a question with more than 1,000 views. For How to prepare trait data file of categorical trait with more than two levels for WGCNA?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to Get and Visualize the Chromosome Physical Position
Popular Question 19 months ago, created a question with more than 1,000 views. For Getting error in running rMATS
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