User: lokraj2003
lokraj2003 • 90
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- lokraj
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Posts by lokraj2003
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... I don't know if it is the right platform to ask this question. But, I could not find any better place than this to ask this question.
I am trying to do some single-cell analysis for a group project. I have about 500 MB of data (count matrixes). I am not able to run any analysis on my PC where I ha ...
written 5 months ago by
lokraj2003 • 90
• updated
5 months ago by
zx8754 ♦ 9.7k
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... Awesome. It works. Actually I have my gene names in the column of a data frame, so this is perfect. Would you mind telling me briefly what these regular expressions are doing? Thanks again for taking your time! ...
written 5 months ago by
lokraj2003 • 90
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... This works. Since, I have all the names in a data frame, the solution provided by @Alex Nemelov suits my need. Thank you! ...
written 5 months ago by
lokraj2003 • 90
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... I want to extract **gene name** , **gene start position** and **gene stop position** from the fasta header of the fasta file. I have tried to extract based on the position but those locations are not consistent. Is there any other way to extract them ?
This is what I have tried so far.
...
written 5 months ago by
lokraj2003 • 90
• updated
5 months ago by
Alex Nesmelov • 170
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... Thanks Brice. I did not split the genome. So, 1250 amino acids was one gene. So, I don't need to adjust my p -value ? Just to confirm I understood your point correctly. ...
written 14 months ago by
lokraj2003 • 90
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... I did selection pressure analysis on viral genomes using MEME, SLAC and FUBAR on Datamonkey server. I am using p value < 0.05 for MEME and SLAC. Do I have to do any type of multiple test correction on the p-value given by MEME and SLAC ? How can I do Bonferroni Test if I have 85 sequences each wi ...
written 14 months ago by
lokraj2003 • 90
• updated
14 months ago by
Brice Sarver • 3.5k
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... Actually it works, but then parsing output became tedious. Thinking of a way to parse the output. ...
written 16 months ago by
lokraj2003 • 90
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... I am going to do selection pressure analysis. So, I will have to do multiple sequence alignment before I could actually do selection pressure analysis. ...
written 16 months ago by
lokraj2003 • 90
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... I have 220 nucleotide sequences. They are around 7000 bp and each of them should translate into one protein of around 2100 amino acids. There are some functions already available in R that can convert nucleotide sequence to amino acid sequence. But, these available functions like `Translate` in `seq ...
written 16 months ago by
lokraj2003 • 90
• updated
16 months ago by
Mensur Dlakic • 7.2k
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... I am trying to learn single cell RNA-Seq data analysis. Right now I am following Seurat and Monocle documentation. I am aware of the fact that we have to create a single cell experiment object, which basically acts as a container for the scRNA data. But, I want make one these container from scratch ...
written 17 months ago by
lokraj2003 • 90
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