User: saamar.rajput

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New User
Location:
Germany
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5 days, 9 hours ago
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2 years, 4 months ago
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Posts by saamar.rajput

<prev • 29 results • page 1 of 3 • next >
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Locate Kegg Pathways from my network
... I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways with the genes in it. But I want to visually see the grouped genes from my network which belong to ...
gene R written 5 days ago by saamar.rajput10 • updated 5 days ago by Jean-Karim Heriche14k
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Reactome Pathway Analysis from command line
... I have a list of genes or may be a file containing a list of genes. I want to see the pathways from Reactome that are enriched with the gene list i have (not just a list of pathway but the visualization from the Reactome Pathway database), But I want to do this by a command line. Is it possible ? I ...
gene rna-seq written 26 days ago by saamar.rajput10
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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 4 months ago by saamar.rajput10 • updated 9 weeks ago by Marks0
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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 5 months ago by saamar.rajput10
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Comment: C: Inserting Noise into RNA-seq raw counts
... What do you suggest then? ...
written 5 months 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 5 months ago by saamar.rajput10
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216
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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 6 months ago by saamar.rajput10 • updated 6 months ago by Devon Ryan76k
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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 15 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 15 months ago by saamar.rajput10 • updated 15 months ago by Charles Plessy2.4k
4
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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 16 months ago by saamar.rajput10 • updated 16 months ago by Jean-Karim Heriche14k

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Supporter 5 months ago, voted at least 25 times.

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