User: Sushant Pawar

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Nashik
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sushant.pawar69
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1 year, 5 months ago
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2 years, 6 months ago
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Posts by Sushant Pawar

<prev • 23 results • page 1 of 3 • next >
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Reading BAM file for RapidR
... Hi all,  I want to read the BAM file in R studio for Package RapdiR using this command. > mask <- "mask.bed" > makeBinnedCountsFile(bam.file.list = c("file1.bam", "file2.bam"), + sampleIDs = c("sample1", "sample2"), + binned.counts.fname = output.fname, + k = 20000) so please tell me wh ...
bam rapidr written 2.3 years ago by Sushant Pawar0 • updated 2.3 years ago by Aaron Lun19k
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Answer: A: about loding BSgenome.Hsapiens.UCSC.hg19 package
... thank you "Martin Morgan" and  "b.nota" problem solve. ...
written 2.3 years ago by Sushant Pawar0
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Loading BSgenome.Hsapiens.UCSC.hg19 package
... Hello friends, unable to load this library. please help me to load this package. source("http://bioconductor.org/biocLite.R") Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help > biocLite("BSgenome.Hsapiens.UCSC.hg19") BioC_mirror: https://bioconductor.org Using Bioconductor 3 ...
ucsc bsgenome.hsapiens.ucsc.hg19 written 2.3 years ago by Sushant Pawar0 • updated 2.3 years ago by Martin Morgan ♦♦ 21k
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Answer: A: List of package names with versions
... you can try this packinfo <- installed.packages(fields = c("Package", "Version")) packinfo[,c("Package", "Version")]   ...
written 2.3 years ago by Sushant Pawar0
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Comment: C: Multiple group analysis
... LRT= Likelihood Ratio Test ...
written 2.3 years ago by Sushant Pawar0
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Comment: C: QC criteria for transcriptome analysis
... Ok Sean i can understand that this is not directly to connected to bioconductor  , but it is primary step for our Bioconductor analysis.  Thank you for your reply ,i will post this question on another site. ...
written 2.4 years ago by Sushant Pawar0
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(Closed) QC criteria for transcriptome analysis
... Hello all,      I have a doubt about the QC criteria for Transcriptome analysis. If we run plugin of ampliseqRNA analysis, What should be the acceptance and rejection criteria from output stats like "Mapped reads", "Valid reads","Target Detected",">=QV 20 Bases,"Bases"  for sample.This output is ...
qc transcriptome written 2.4 years ago by Sushant Pawar0
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edgeR with unequal no.of replicate
... Hi all,     I am using edgeR for Gene expression analysis. My question is about unequal no.of replicate. If we have 4 replicate of Control and 1 Case Sample then is it fair to do analysis or we should go with edgeR without replicate like 1 case and 1 Control. ...
edger replicate written 2.4 years ago by Sushant Pawar0 • updated 20 months ago by nancyjwahl70
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Comment: C: edgeR Code syntax for without replicate
... Hello Aaron , Thank you for your support. i have done with the "fdr" command please once again go through it. And suggest if any thing require to complete the programme. =============================================== library(edgeR) Read_counts=read.delim("Table.txt",row.names = "Gene") counts= ...
written 2.5 years ago by Sushant Pawar0
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Comment: C: edgeR Code syntax for without replicate
... Dear Aaron, Thank you for reply. I have add the syntax that you have suggested , And "Output<- topTags(et, n=Inf, sort.by="none")$table" will be my final  table for further analysis please take a look at syntax once again. =============================================================== libr ...
written 2.5 years ago by Sushant Pawar0

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