User: Sushant Pawar

Reputation:
0
Status:
New User
Location:
Nashik
Twitter:
sushant.pawar69
Last seen:
10 months, 1 week ago
Joined:
1 year, 11 months ago
Email:
b******@datarpgx.org

Posts by Sushant Pawar

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answer
387
views
1
answer
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 20 months ago by Sushant Pawar0 • updated 20 months ago by Aaron Lun17k
0
votes
1
answers
677
views
1
answers
Answer: A: about loding BSgenome.Hsapiens.UCSC.hg19 package
... thank you "Martin Morgan" and  "b.nota" problem solve. ...
written 20 months ago by Sushant Pawar0
2
votes
1
answer
677
views
1
answer
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 20 months ago by Sushant Pawar0 • updated 20 months ago by Martin Morgan ♦♦ 20k
0
votes
1
answers
373
views
1
answers
Answer: A: List of package names with versions
... you can try this packinfo <- installed.packages(fields = c("Package", "Version")) packinfo[,c("Package", "Version")]   ...
written 21 months ago by Sushant Pawar0
0
votes
2
answers
421
views
2
answers
Comment: C: Multiple group analysis
... LRT= Likelihood Ratio Test ...
written 21 months ago by Sushant Pawar0
0
votes
0
answers
263
views
0
answers
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 22 months ago by Sushant Pawar0
0
votes
0
answers
263
views
0
answers
(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 22 months ago by Sushant Pawar0
2
votes
2
answers
440
views
2
answers
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 22 months ago by Sushant Pawar0 • updated 13 months ago by nancyjwahl70
0
votes
1
answers
575
views
1
answers
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 23 months ago by Sushant Pawar0
0
votes
1
answers
575
views
1
answers
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 23 months ago by Sushant Pawar0

Latest awards to Sushant Pawar

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 211 users visited in the last hour