User: arup

gravatar for arup
arup490
Reputation:
490
Status:
Trusted
Location:
India
Website:
http://arupgsh.github.io/
Twitter:
arupgsh
Scholar ID:
Google Scholar Page
Last seen:
5 days, 15 hours ago
Joined:
2 years, 10 months ago
Email:
a*******@gmail.com

PhD student @ Institute of Life Science, Bhubaneswar

Posts by arup

<prev • 93 results • page 1 of 10 • next >
0
votes
1
answer
78
views
1
answers
Comment: A: Submit High-Throughput data to GEO. Problems with FTP connection
... Submit your data to ArrayExpress, it has a better interface for metadata management and file uploading. The direct FTP connection is also fast, accession ids are provided within a couple of hours and with a week they will provide the reviewer account details. ...
written 8 days ago by arup490
1
vote
1
answer
147
views
1
answers
Answer: A: loaded a sorted bam file in IGV but I can't see anything
... Salmon is a pseudoaligner so clearly, the output you are getting does not have mapping information. Try `--writeMappings` argument to include the alignment information. Ref: https://salmon.readthedocs.io/en/latest/salmon.html ...
written 8 days ago by arup490
0
votes
1
answer
215
views
1
answers
Comment: C: SNPs annotations tool
... Can you elaborate "good and reliable"? ...
written 7 weeks ago by arup490
0
votes
1
answer
222
views
1
answers
Comment: C: annotatePeaks.pl without annotation in genes name
... Please share the command you have used. ...
written 9 weeks ago by arup490
0
votes
1
answer
260
views
1
answers
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 11 weeks ago by arup490
0
votes
7
answers
2.9k
views
7
answers
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 11 weeks ago by arup490
0
votes
1
answer
204
views
1
answers
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 11 weeks ago by arup490
0
votes
0
answers
167
views
0
answers
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 11 weeks ago by arup490
0
votes
0
answers
167
views
0
answers
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 11 weeks ago by arup490
1
vote
0
answers
270
views
0
answers
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 11 weeks ago by arup490

Latest awards to arup

Voter 15 days ago, voted more than 100 times.
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 3 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 8 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Supporter 8 months ago, voted at least 25 times.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1695 users visited in the last hour