User: c.chakraborty

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c.chakraborty100
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Posts by c.chakraborty

<prev • 28 results • page 1 of 3 • next >
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Answer: A: Where Can I find protein-protein interactions data ?
... Try STRING db for networks ...
written 2 days ago by c.chakraborty100
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Answer: A: Panther pathway gene list counts
... I am not sure if this helps or not, but since the GOIDs are from GO consortium, maybe you can search for the GO term of your interest say- GO:0043066, and then this navigates you to the page with links to gene and gene products, ontology etc. And from there you can select gene and gene products and ...
written 2 days ago by c.chakraborty100
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Answer: A: gene expression analysis using RNA seq data
... Hey I am adding these links so you can go through to understand the normalization of FPKM/RPKM and TPM- https://statquest.org/2015/07/09/rpkm-fpkm-and-tpm-clearly-explained/ https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ FPKM of a gene (say ABB) is ...
written 7 weeks ago by c.chakraborty100
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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 3 months ago by c.chakraborty100
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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 3 months ago by c.chakraborty100
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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 3 months ago by c.chakraborty100 • updated 3 months ago by zx87545.6k
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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 3 months ago by c.chakraborty100 • updated 3 months ago by zx87545.6k
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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 4 months ago by c.chakraborty100
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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 4 months ago by c.chakraborty100 • updated 4 months ago by h.mon21k
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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 4 months ago by c.chakraborty100 • updated 4 months ago by h.mon21k

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