User: Pappu
Pappu • 1.9k
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Posts by Pappu
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22
votes
5
answers
450
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
230
views
1
answers
... Human gencode outputs ~60k genes. ...
written 12 months ago by
Pappu • 1.9k
2
votes
1
answer
230
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 12 months ago by
Pappu • 1.9k
0
votes
0
answers
443
views
0
answers
Comment:
C: Gene function prediction
... Nothing came out from uniprot go annotation. ...
written 19 months ago by
Pappu • 1.9k
0
votes
0
answers
443
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 19 months ago by
Pappu • 1.9k
0
votes
0
answers
287
views
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 19 months ago by
Pappu • 1.9k
2
votes
0
answers
469
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 19 months ago by
Pappu • 1.9k
3
votes
0
answers
909
views
0
answers
... I am wondering if there is any curated list of top cited bioinformatics papers during last 5 years.. ...
written 20 months ago by
Pappu • 1.9k
1
vote
1
answer
579
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
325
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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