User: EagleEye
EagleEye • 4.2k
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Investigating field of biology by applying logics of computer science, statistics and mathematics.
Posts by EagleEye
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[GeneSCF][1]
[1]: https://www.biostars.org/p/108669/ ...
written 15 hours ago by
EagleEye • 4.2k
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... May I know how you say Refseq as 'high quality set' (in which context) ??
Did you first of all check the links I provided ? All those repositories are standard repositories used for lncRNA analysis.
If you want information on refseq genes check [Refseq FTP][1]
[1]: ftp://ftp.ncbi.nlm.nih.gov/ ...
written 23 hours ago by
EagleEye • 4.2k
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I guess you are looking for [OncoPrint][1]
[1]: https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html ...
written 1 day ago by
EagleEye • 4.2k
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... I can suggest you to use,
1) Gencode 'Long non-coding RNA gene annotation'
http://www.gencodegenes.org/releases/current.html
2) Ensembl (Extract only lincRNA)
ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/
3) noncode
http://www.noncode.org/download.php
4) FANTOM CAT
http://fantom. ...
written 1 day ago by
EagleEye • 4.2k
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Take a look at [GeneSCF][1].
[1]: https://www.biostars.org/p/108669/ ...
written 3 days ago by
EagleEye • 4.2k
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3
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BED tools [Closest][1]
[1]: http://bedtools.readthedocs.io/en/latest/content/tools/closest.html ...
written 4 days ago by
EagleEye • 4.2k
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... Sorry non-R solution:
With [GeneSCF][1] you can keep all the list of genes (multiple files) in a single folder and provide that path in '**geneSCF_batch**'. It will perform enrichment analysis for individual list and automatically creats output for every list.
Also choose the tool that regularly u ...
written 4 days ago by
EagleEye • 4.2k
0
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... Hi, [GeneSCF][1]: You can retrieve the current data from the repository. GeneSCF is specially designed for that.
[1]: https://www.biostars.org/p/108669/ ...
written 5 days ago by
EagleEye • 4.2k
0
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... Sorry I do not have any solution in R. All the best for you to solve your task. ...
written 6 days ago by
EagleEye • 4.2k
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... Use geneontology GO_CC in [GeneSCF][1] enrichment analysis.
[1]: https://www.biostars.org/p/108669/ ...
written 6 days ago by
EagleEye • 4.2k
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