User: kirannbishwa01

gravatar for kirannbishwa01
Reputation:
0
Status:
New User
Location:
Last seen:
1 week, 3 days ago
Joined:
1 year, 2 months ago
Email:
k*************@gmail.com

Posts by kirannbishwa01

<prev • 6 results • page 1 of 1 • next >
2
votes
1
answer
361
views
1
answer
enrichGO from DOSE, clusterprofiler is returning empty result.
... I am trying to use enrichGO function from clusterProfiler package. All is good except that my results are empty. # for significant genes > sig.foldChangesAbv2 %>% length() [1] 244 > sig.foldChanges %>% head(5) [1] "NA1"       "AT1G64640" "AT1G64630" "AT1G64625" "NA3" # for universal ...
annotation clusterprofiler dose gene ontology gene set enrichment written 8 months ago by kirannbishwa01 • 0 • updated 8 months ago by Guangchuang Yu • 1.0k
0
votes
1
answer
301
views
1
answer
How to name the custom genome in karyoploteR ?
... I really like the features that are provided in karyoploteR. https://bioconductor.org/packages/release/bioc/html/karyoploteR.html But, I am working with different organisms. I am able to find the organisms of interest using: > available.genomes()  [1] "BSgenome.Alyrata.JGI.v1"                 ...
bsgenome software error R karyoploter written 8 months ago by kirannbishwa01 • 0 • updated 8 months ago by bernatgel • 90
0
votes
2
answers
326
views
2
answers
Comment: C: Add new columns to DESeqResults from text file by matching rownames.
... Hi Steve, I knew about this method, but the problem is that if you convert the S4-object using as.data.frame you are loosing valuable metadata information that are used downstream in the workflow. Any other ideas.   ...
written 9 months ago by kirannbishwa01 • 0
0
votes
3
answers
5.8k
views
3
answers
Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
... HI Michael, If your time allows, Can you please look into this problem? https://support.bioconductor.org/p/101008/ ...
written 9 months ago by kirannbishwa01 • 0
4
votes
2
answers
326
views
2
answers
Add new columns to DESeqResults from text file by matching rownames.
... I have generated results from DESeq2 wihch is a S4 type R-object. I want to add new columns to it containing geneNames, contig and start position. There is method using BioMart to do it, but I won't be using the BioMart method; instead I have the geneDatabase as a textfile, I have tried merging th ...
deseq deseq2 s4vectors cbind merge data frames written 9 months ago by kirannbishwa01 • 0 • updated 9 months ago by Michael Love ♦ 18k
0
votes
2
answers
1.6k
views
2
answers
Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
... HI @Aaron: What do you mean by, "Dropping it will test for allele-specific expression, averaged across all individuals"? Are we not supposed to keep the design as it is as ~0+individual+allele   ...
written 9 months ago by kirannbishwa01 • 0

Latest awards to kirannbishwa01

No awards yet. Soon to come :-)
Content
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