User: Bioinformatics

Reputation:
30
Status:
New User
Location:
Last seen:
2 days, 11 hours ago
Joined:
3 years, 5 months ago
Email:
m************@gmail.com

Posts by Bioinformatics

<prev • 67 results • page 1 of 7 • next >
0
votes
0
answers
50
views
0
answers
Comment: C: how can I find a pathway
... @mahmoud.s.fahmy finding which pathways those molecules are belonging to ...
written 6 days ago by Bioinformatics30
0
votes
0
answers
50
views
0
answers
how can I find a pathway
... I have a Metabolomics data with a p value, I want to know which ways I can find pathways, as an example please use the following data df<- structure(list(rn = c("1-Methylhistidine", "L-Kynurenine", "N6,N6,N6-Trimethyl-L-lysine", "Putrescine", "Cytidine", "Xanthosine", "N-Alpha-acetyllys ...
keggrest kegg written 11 days ago by Bioinformatics30
1
vote
1
answer
124
views
1
answer
how can I convert a sequence to number
... I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number https://www.bioconductor.org/packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino- ...
motifstack written 8 months ago by Bioinformatics30 • updated 8 months ago by Ou, Jianhong1.2k
0
votes
2
answers
290
views
2
answers
Comment: C: how can I calculate FDR with no replicate
... @Aaron Lun Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 10 months ago by Bioinformatics30
0
votes
2
answers
290
views
2
answers
Comment: C: how can I calculate FDR with no replicate
... @Gordon Smyth Look at this manuscript somewhat got me thinking https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287564/ ...
written 10 months ago by Bioinformatics30
0
votes
2
answers
290
views
2
answers
Comment: C: how can I calculate FDR with no replicate
... @ Aaron Lun I did read that part for sure, I cannot estimate the dispersion because I don't have many housekeeping genes so I set it as 0.4 which I think it is a good number between 0.1 and 0.6. Yes ` estimateGLMCommonDisp` does not work due to problem you mentioned. I am just wondering if there i ...
written 10 months ago by Bioinformatics30
0
votes
2
answers
290
views
2
answers
Comment: C: how can I calculate FDR with no replicate
... @Gordon Smyth these are normalized expression not count. so it means if people do not use raw count, it won't be trusted? I have read many papers they published in science with FMPK which is normalized count by length of gene analyzed by edger !! (I personally do not like FMPK but just as example. ...
written 10 months ago by Bioinformatics30
1
vote
2
answers
290
views
2
answers
how can I calculate FDR with no replicate
... Hi, I have a representative data like this. the first column is control and second is treated df<- structure(list(col1A = c(1.64, 0.03, 0, 4.202, 2.981, 0.055, 0, 0.002, 0.005, 0, 0.002, 0.649, 2.55, 2.762, 6.402, 0.91, 0.037, 0, 5.757, 3.916, 0.022, 0, 0, 0.003, 0, 0.262, 0.136, ...
microarray edger written 10 months ago by Bioinformatics30 • updated 10 months ago by Gordon Smyth39k
0
votes
1
answer
365
views
1
answers
Comment: C: how to retrieve all attributes from biomart ?
... @James W. MacDonald gene ontology means you can find various information from any given gene. Look at http://www.geneontology.org    ...
written 12 months ago by Bioinformatics30
0
votes
1
answer
365
views
1
answers
Comment: C: how to retrieve all attributes from biomart ?
... @James W. MacDonald basically I am trying to do gene onthology. there are 100 packages but I prefer to retrieve data from UniProt or ensemble.  ...
written 12 months ago by Bioinformatics30

Latest awards to Bioinformatics

Popular Question 2.5 years ago, created a question with more than 1,000 views. For unable to update packages: foreign, Matrix

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 293 users visited in the last hour