User: c.chakraborty

gravatar for c.chakraborty
Reputation:
80
Status:
Trusted
Location:
Last seen:
5 hours ago
Joined:
9 months ago
Email:
c************@cent.uw.edu.pl

Posts by c.chakraborty

<prev • 25 results • page 1 of 3 • next >
0
votes
1
answer
125
views
1
answers
Comment: C: Gene (mRNA) - Protein Interaction databases and prediction
... I am not really sure if there is one golden standard rule to do it. But, if I have to do this, I will find what motifs do my RBPs have and search literature for the sequences that these motifs can bind to, say a motif recognizes AU rich sequences. Then I record the sequence of that motif or motifs ...
written 7 weeks ago by c.chakraborty80
0
votes
1
answer
125
views
1
answers
Answer: A: Gene (mRNA) - Protein Interaction databases and prediction
... I found these two- http://pri.hgc.jp/ http://lulab.life.tsinghua.edu.cn/postar2/rbp2.php But, I am not sure about reliability. Usually RBPs interact mRNAs with specific domains like RRMs, zinc-fingers etc. If I know which domain my protein has, I would data-mine literature to get probable RNA bindin ...
written 7 weeks ago by c.chakraborty80
1
vote
2
answers
118
views
2
answers
Answer: C: equal distance between groups in a barplot
... Problem solved: barplot(david_go__ord_foldenr$Fold.Enrichment, names.arg = david_go__ord_foldenr$Description, horiz = TRUE, space = 0.1, cex.names = 0.5, cex.axis = 0.6, col = "blue", xlim = c(0,3)) ...
written 8 weeks ago by c.chakraborty80 • updated 8 weeks ago by zx87544.9k
3
votes
2
answers
118
views
2
answers
Equal distance between groups in a barplot
... I have a very simple question and I have been quite unable to find a suitable answer. I am making barplots for GO-enriched terms- barplot(Fold.Enrichment, names.arg = Description, horiz = TRUE, cex.names = 0.5, cex.axis = 0.6, col = "b ...
R written 8 weeks ago by c.chakraborty80 • updated 8 weeks ago by zx87544.9k
0
votes
1
answer
169
views
1
answers
Comment: C: length of a DNAString
... This is great, thanks a bunch! I also found a crude solution. If I load the files by ape and then unlist it, and then ask for length, it works! ...
written 9 weeks ago by c.chakraborty80
2
votes
1
answer
169
views
1
answer
length of a DNAString
... I am doing something extremely basic and stupid. I can call a fasta seq using this x <- readDNAStringSet(file.choose()) file gets opened, and then I type this length(x) [1] 1 But when I use view, I can see nicely that it has 11405 bp. I can use seqinr to get the length, like lengt ...
using readdnastringset- R biostrings written 9 weeks ago by c.chakraborty80 • updated 9 weeks ago by h.mon19k
0
votes
0
answers
117
views
0
answers
ArrayExpress dataset error
... I am having a small problem, and I would like to know what is the one stupid thing I am doing- I am trying to look for datasets for mouse brain in arrayexpress database through R and I am getting an error- My code- sets = queryAE(keywords = "brain", species = "mus+musculus") > curl: (1) Pro ...
R arrayexpress written 10 weeks ago by c.chakraborty80 • updated 10 weeks ago by h.mon19k
0
votes
1
answer
156
views
1
answers
Answer: A: combine RNA-seq data count and len
... You can upload both the files in R, and then create a data frame with transcription ID, gene.length, and read.counts together. Use reshape2 and plyr for merging the files. Check this link https://www.biostars.org/p/126316/ ...
written 12 weeks ago by c.chakraborty80
0
votes
3
answers
212
views
3
answers
Answer: A: Pathway enrichment analysis of gene set
... You can also upload your gene list to MSigDB and look for Pathway enrichment. ...
written 12 weeks ago by c.chakraborty80
0
votes
1
answer
231
views
1
answers
Answer: A: GSEA Phenotype Table Input
... Hey, I am not sure, if I am answering you properly, but when you do diferential gene expression analysis using DEseq2, you will get hits which are definitely biassed for the sex factor. In such a condition, I would try to look for raw data from Array Express or GeoOmnibus,for male wild-type and fem ...
written 3 months ago by c.chakraborty80

Latest awards to c.chakraborty

Supporter 4 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1435 users visited in the last hour