User: piyushjo
piyushjo • 160
- Reputation:
- 160
- Status:
- Trusted
- Location:
- Last seen:
- an hour ago
- Joined:
- 1 year, 3 months ago
- Email:
- p*******@gmail.com
Posts by piyushjo
<prev
• 73 results •
page 1 of 8 •
next >
0
votes
2
answers
113
views
2
answers
... Could list at least 5 examples of genbank and other gene id you are referring to? ...
written 1 day ago by
piyushjo • 160
0
votes
2
answers
80
views
2
answers
... You can try WGCNA. It will help you select non-linearly correlated genes. I am just concerned with such a small sample cohort you have.
https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/
For your second analysis you can use mutual information based analysis. For that you ...
written 1 day ago by
piyushjo • 160
0
votes
2
answers
113
views
2
answers
... Yes, sorry. It looks like while ensembl has a page your organism it doesn't show up in the biomart.
http://bacteria.ensembl.org/Pseudomonas_aeruginosa_pa14/Info/Index ...
written 1 day ago by
piyushjo • 160
0
votes
2
answers
113
views
2
answers
... Biomart from ensembl.org has such features. You can convert any given id to another id. I see the you organism has an ensembl page. I think you could use the biomaRt package in R and follow the example for human data from below vignette.
https://bioconductor.org/packages/release/bioc/vignettes/bio ...
written 1 day ago by
piyushjo • 160
0
votes
2
answers
125
views
2
answers
... You can follow the instruction on the following webpage with the heading "Loading matrices into R".
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices
It will generate what is called a "sparse-matrix".
Then you convert the sparse-matrix (SM) into ...
written 1 day ago by
piyushjo • 160
2
votes
1
answer
57
views
1
answers
... One way to do it is to use STRINGdb. They have various type of interaction information. The annotation will also tell you what the presumed interaction is and the level of evidence.
The second is to use Ingeniuty Pathway Analysis. However, this is a paid service. You can get similar information, bu ...
written 2 days ago by
piyushjo • 160
2
votes
2
answers
91
views
2
answers
... Try biomart.
Website
https://useast.ensembl.org/info/data/biomart/index.html
R package
https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html
Use Gene symbol as filter and then entrez id as attribute.
...
written 7 days ago by
piyushjo • 160
0
votes
2
answers
95
views
2
answers
... You first need to have files with those name in the folder. list1 and list2 are the two lists that have given in your example.
...
written 9 days ago by
piyushjo • 160
0
votes
2
answers
95
views
2
answers
... You have to add description as a comment and not as answer. ...
written 10 days ago by
piyushjo • 160
0
votes
2
answers
95
views
2
answers
... Try this
list1<-read.delim("1_10.txt")
list2<-read.delim("1_10.txt")
Here both of your lists are exactly same. Do you have long list of genes in two files or is it a matrix? The following will work for a list with one column.
First convert factors into characters array
list1&l ...
written 10 days ago by
piyushjo • 160
Latest awards to piyushjo
Scholar
3 days ago,
created an answer that has been accepted.
For A: Get a bunch of ENTREZID into gene symbols
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How different is rlog transformation from vst transformation in DESeq2
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1613 users visited in the last hour