User: saamar.rajput

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Germany
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Posts by saamar.rajput

<prev • 27 results • page 1 of 3 • next >
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FDR and Pvalue in EdgeR
... I am doing differential expression analysis on my data. I am getting all the results i want except for the FDR value. I want to know both the pvalue for the gene and the adjp for the gene. How to get that ? here is my code and my result exprs <- as.matrix(read.table(exprsFile, header ...
R rna-seq written 8 weeks ago by saamar.rajput10 • updated 8 weeks ago by Nicolas Rosewick5.7k
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(Closed) Adding shot Noise to RNAseq counts
... I want to add Shot Noise in my RNAseq counts data, does anybody know how to do that? ...
rna-seq written 10 weeks ago by saamar.rajput10
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Comment: C: Inserting Noise into RNA-seq raw counts
... What do you suggest then? ...
written 10 weeks ago by saamar.rajput10
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Inserting Noise into RNA-seq raw counts
... I have a RNA-seq raw counts data and I want to test a software for which i want to compare the results of data with noise and data without noise in the counts. For this i need to add some noise into my RNA-seq raw counts data. Can somebody suggest how to add noise into my data at the transcript cou ...
next-gen rna-seq written 10 weeks ago by saamar.rajput10
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Extracting selected gene interaction from an interanction file
... I have a text file "Interaction" with gene gene interactions in this format a1cf apobec1 a1cf ep300 a2m actb a2m ambp a2m apoa1 a2m app a2m bmp1 a2m cdc42 a2m f2 a2m ep300 The first column is the source and the second column ...
gene R rna-seq written 3 months ago by saamar.rajput10 • updated 3 months ago by Devon Ryan73k
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Comment: C: Extract Information from fasta File
... this is the output >ENST00000448914.1 ENSG00000228985.1 ACTGGGGGATACG ACTGGGGGATACG >ENST00000631435.1 ENSG00000282253.1 GGGACAGGGGGC GGGACAGGGGGC >ENST00000632684.1 ENSG00000282431.1 GGGACAGGGGGC GGGACAGGGGGC i do not need the sequence after the gene information bu ...
written 12 months ago by saamar.rajput10
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Extract Information from fasta File
... I have big fasta file with information like this, >ENST00000448914.1 cdna chromosome:GRCh38:14:22449113:22449125:1 gene:ENSG00000228985.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:TRDD3 description:T cell receptor delta diversity 3 [Source:HGNC Symbol;Acc:HGNC:12256] ...
genome gene rna-seq written 12 months ago by saamar.rajput10 • updated 12 months ago by Charles Plessy2.3k
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Constant layout orientation in igraph
... I am drwaning graphs in igraph using the "layout_with_dh" layout, but everytime i generate the graph the orientation is changed. Is there a way to keep the same orientation of the graph as i would be looking at the graph for different timepoints so I want them to look the same. ...
R rna-seq written 13 months ago by saamar.rajput10 • updated 13 months ago by Jean-Karim Heriche13k
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Comment: C: KEGG graph not completely connected
... I am working on Homosapiens pathways especially Salmonella infection. It is not a completely connected graph. ...
written 13 months ago by saamar.rajput10
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Keep the KEGG coordinates while passing KEGG pathway (graphNEL) to igraph
... Hello Everyone, I downloaded the KEGG pathway using the parseKGML2Graph FUNCTION and when i plot the graph directly it shows a nice graph with KEGG coordinates, But when i convert the graphNEL object to igraph using igraph.from.graphNEL , it loses it coordinates. I want the same coordinates as KEG ...
R kegg igraph written 14 months ago by saamar.rajput10 • updated 13 months ago by Biostar ♦♦ 20

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Supporter 10 weeks ago, voted at least 25 times.

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