User: arup

gravatar for arup
arup470
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

<prev • 90 results • page 1 of 9 • next >
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Comment: C: annotatePeaks.pl without annotation in genes name
... Please share the command you have used. ...
written 6 days ago by arup470
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Comment: C: Gene Set Enrichment between two dataset
... 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 arup470
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Comment: C: Where can I find public Single Cell RNA-seq data?
... Try http://www.cellatlassearch.com/ if you are looking for human scRNA-seq samples. ...
written 20 days ago by arup470
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Comment: C: micro-array analysis without FoldChange
... 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 arup470
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Comment: C: Differential expression analysis suggestions needed
... You should avoid using cufflinks & tophat, any other analysis flow will be fine. https://twitter.com/lpachter/status/937055346987712512 ...
written 20 days ago by arup470
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Comment: C: Differential expression analysis suggestions needed
... 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 arup470
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Comment: C: NCBI esearch for cited papers with public SRA data
... 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 arup470
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Comment: C: conda tophat installation error
... Go for a faster aligner like Hisat2, Star etc. ...
written 21 days ago by arup470
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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 arup470
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Answer: A: removing outliers before running DESeq2
... 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 arup470

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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