User: Pappu
Pappu • 1.9k
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Posts by Pappu
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22
votes
5
answers
390
views
10 follow
5
answers
... I am wondering which productivity tools you use as a bioinformatician to improve the productivity of day to day work. For example using git, nextflow etc. ...
0
votes
1
answer
190
views
1
answers
... Human gencode outputs ~60k genes. ...
written 9 months ago by
Pappu • 1.9k
2
votes
1
answer
190
views
1
answer
... I am wondering if it is a standard practice to only include ~20k protein coding genes for DE and subsequent pathway analysis? ...
written 9 months ago by
Pappu • 1.9k
0
votes
0
answers
404
views
0
answers
Comment:
C: Gene function prediction
... Nothing came out from uniprot go annotation. ...
written 15 months ago by
Pappu • 1.9k
0
votes
0
answers
404
views
0
answers
... I am wondering if there is any good way to predict the function of a gene given the fact that hardly any literature exists on it. ...
written 15 months ago by
Pappu • 1.9k
0
votes
0
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258
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0
answers
... I am looking for a list of differentially expressed (up and down) genes from all cmap perturbation experiments at clue.io I could only get a small fraction of those from the Enrichr website. I am wondering where can I get such list or how can I generate it from the raw data? ...
written 15 months ago by
Pappu • 1.9k
2
votes
0
answers
431
views
5 follow
0
answers
... I am wondering if the is any basic experimental methods book or review for bioinformaticians so that they can understand the presentations given by experimentalists. Such book should include what kind of experimental methods can be used to validate what kind of in-silico analysis results for example ...
written 16 months ago by
Pappu • 1.9k
3
votes
0
answers
786
views
0
answers
... I am wondering if there is any curated list of top cited bioinformatics papers during last 5 years.. ...
written 16 months ago by
Pappu • 1.9k
1
vote
1
answer
487
views
1
answer
... I am wondering if there is any pipeline which runs DESeq2, EdgeR etc DE analysis and GSEA, Pathway etc enrichment and other basic analysis in one go and make the results available by some kind of shiny or other web app. ...
4
votes
0
answers
294
views
0
answers
... I am wondering what is the effect of following filters before using fast quantifiers like salmon/kallisto:
1. Adapter trimming
2. Size selection
3. Quality filtering ...
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