User: arup
arup • 470
- Reputation:
- 470
- Status:
- Trusted
- Location:
- India
- Website:
- http://arupgsh.github.io/
- Twitter:
- arupgsh
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 hours ago
- Joined:
- 2 years, 8 months ago
- Email:
- a*******@gmail.com
PhD student @ Institute of Life Science, Bhubaneswar
Posts by arup
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... Please share the command you have used. ...
written 6 days ago by
arup • 470
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... The following tools will be helpful to achieve that.
https://bioconductor.org/packages/release/bioc/html/GSEABase.html
https://bioconductor.org/packages/release/bioc/html/fgsea.html
...
written 17 days ago by
arup • 470
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... Try http://www.cellatlassearch.com/ if you are looking for human scRNA-seq samples. ...
written 20 days ago by
arup • 470
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... if you have the data reanalyze it. Without the fold change you can't extract "up or down-regulated" genes, as both up and down-regulated genes can have the same level of significance. ...
written 20 days ago by
arup • 470
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... You should avoid using cufflinks & tophat, any other analysis flow will be fine.
https://twitter.com/lpachter/status/937055346987712512 ...
written 20 days ago by
arup • 470
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... https://cgatoxford.wordpress.com/2016/08/17/why-you-should-stop-using-featurecounts-htseq-or-cufflinks2-and-start-using-kallisto-salmon-or-sailfish/ ...
written 20 days ago by
arup • 470
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... This [python script][1] can automate the process but it'll throw an error when `get_sra_ids(pmid) ` encounters an article with no linked SRA ids because of missing `[u'LinkSetDb'][0][u'Link']` tag on those entries. The same may happen with `get_citations(pmid)` .
[1]: https://github.com/arupgsh ...
written 20 days ago by
arup • 470
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Comment:
C: conda tophat installation error
... Go for a faster aligner like Hisat2, Star etc. ...
written 21 days ago by
arup • 470
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Comment:
C: The interpretation of PCA
... Check out this detailed PC analysis article by Markus Ringnér,
https://www.nature.com/articles/nbt0308-303 ...
written 23 days ago by
arup • 470
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... There is no need to remove out layers but it's better to remove the technical artifacts(noise incorporated by the sequencer). Genes/transcripts having read count within 0-10 rage is generally considered as artifacts(if the expression pattern is inconstant throughout all the samples). For more detail ...
written 23 days ago by
arup • 470
Latest awards to arup
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: How can I uninstall my packages in Rstudio
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar
6 months ago,
created an answer that has been accepted.
For A: How can I uninstall my packages in Rstudio
Supporter
6 months ago,
voted at least 25 times.
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Visualising BedGraph files on UCSC [custom tracks]
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