User: c.chakraborty

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Posts by c.chakraborty

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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 7 days ago by c.chakraborty70
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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 8 days ago by c.chakraborty70 • updated 7 days ago by h.mon16k
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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 14 days ago by c.chakraborty70 • updated 13 days ago by h.mon16k
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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 27 days ago by c.chakraborty70
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Answer: A: Pathway enrichment analysis of gene set
... You can also upload your gene list to MSigDB and look for Pathway enrichment. ...
written 27 days ago by c.chakraborty70
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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 4 weeks ago by c.chakraborty70
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Answer: A: How to find common data in replicates?
... We can use Excel, *VLOOKUP*, for each identifier for each of the arrays, and then `VLOOKUP` for the values in each array- ID Val1 Val2 Val3 Abc =VLOOKUP(cellA1, from array.csv rep1 col A:B, return value of cell B, False) Def Ghi and so on and you can get the valu ...
written 4 weeks ago by c.chakraborty70 • updated 4 weeks ago by zx87544.7k
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Answer: A: Human Gene Regulatory Database
... You can also view the regulatory tract of the genomic region you're interested at the UCSC genome browser. Scroll down to "Expression and Regulation", and by selecting different datasets (based on the study you're interested in) you can assess the location of promoters, TFBS motifs and methylation/a ...
written 9 weeks ago by c.chakraborty70
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Answer: A: Protein classification system
... Well your study is quite wide. Because, I am not sure you will find something, say motif or domain absolutely common to all proteins. You can pick a class, say polymerases, membrane proteins, metabolic pathway enzymes, and then study their topology, abundance and functional motifs. This way it would ...
written 3 months ago by c.chakraborty70
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Answer: A: DNA Motif discovery from a large number of FASTA sequences
... Hey if you are looking for motif enrichment use centrimo or MEME-ChIP, because there you can upload you sequences from DEG and unchanged genes and look for Transcription factor binding sites, for example or for miR datasets. If you are using MEME or any othe above mentioned tools, you can use the ou ...
written 3 months ago by c.chakraborty70

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