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User: pradyumna Jayaram

gravatar for pradyumna Jayaram
Reputation:
20
Status:
New User
Location:
Manipal, School Of Life Sciences
Last seen:
3 days, 4 hours ago
Joined:
3 years, 3 months ago
Email:
p**********@learner.manipal.edu

Posts by pradyumna Jayaram

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Differential gene expression Analysis - sample Size
... great! Thank you very much. ...
written 9 days ago by pradyumna Jayaram • 20
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Comment: C: Differential gene expression Analysis - sample Size
... Can we compare 3 normal with 300 tumor sample? CESC in TCGA has only 3 normal samples. ...
written 12 days ago by pradyumna Jayaram • 20
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Comment: C: How to take input TCGA miRNA data in Limma R package for differential expression
... It seems like the data is for single sample. the same read count is available for multiple samples and can be merged. I'm Guessing to go with DESeq2 or EdgeR for differential analysis. can limma be used for same? which one would be more effitient in identifying differential expression? ...
written 24 days ago by pradyumna Jayaram • 20
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Comment: C: How to take input TCGA miRNA data in Limma R package for differential expression
... @kevin Yes it is miRNA-seq data from TCGA ...
written 24 days ago by pradyumna Jayaram • 20
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Comment: C: How to take input TCGA miRNA data in Limma R package for differential expression
... Hi, @skjobs1234 did you find an appropriate answer for your query? Even I'm performing the similar analysis. ...
written 24 days ago by pradyumna Jayaram • 20
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Comment: C: Tools for Copy Number Variation analysis from ion Proton data.
... I have 10 samples and 1 pooled Control sample will it work good? ...
written 11 months ago by pradyumna Jayaram • 20
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Tools for Copy Number Variation analysis from ion Proton data.
... Hello Everyone, Can anyone suggest the tool to detection of copy number variation from the data obtained from Ampliseq exome sequencing Iontorrent proton platform. I have tried different tools like Excavator2, cnvkit, FreeC, Ionreporter. Each tool gives different region of CNV from the data. ...
iontorrent-proton ampliseq ngs next-gen cnv written 11 months ago by pradyumna Jayaram • 20 • updated 11 months ago by erwan.scaon • 570
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Comment: C: Looking for wig base coverage file for hg19
... Excavator2_v1.1.2 provides ucsc.hg19.bw file, I think you can use ucsc's bigWigToWig utility to convert. I am not sure whether it is a good choice. ...
written 11 months ago by pradyumna Jayaram • 20
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Comment: C: How to run EXCAVATOR2?
... Hi, I just found out that the issue was with the R script in package and the R version I am using. The problem was resolved by changing na.rm value from `na.rm=T` to `na.rm=TRUE` in all the scripts. ...
written 12 months ago by pradyumna Jayaram • 20
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How to run EXCAVATOR2?
... I have downloaded and installed all the dependencies for excavator2 tool, I have created the target, and while creating data prepare step I ran the following command `perl EXCAVATORDataPrepare.pl melas_prepare.txt --processors 6 --target melas20k --assembly hg19` I got the following error: ...
R excavator2 written 13 months ago by pradyumna Jayaram • 20

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