User: elsoja

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elsoja110
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Posts by elsoja

<prev • 34 results • page 2 of 4 • next >
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Answer: A: How to extract lncRNA from CPC2 output?
... I'd suggest you not to use CPC2 because there are several better performing alternatives out there. I've developed RNAsamba, a software that has the same purpose of CPC2 with a much higher classification performance. You can use it online here: https://rnasamba.lge.ibi.unicamp.br/ As for your quest ...
written 8 months ago by elsoja110
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Answer: A: Software and algorithm for identification of tissue-specific express genes
... If you're looking for a database of expression patterns, including tissue-specificity, you can take a look at [PaGenBase][1]. In case you want to identify tissue-specific genes in your own data, you can use [tspex][2], a tool that I've developed. It offers a variety of tissue-specificity metrics, in ...
written 12 months ago by elsoja110
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Comment: C: How to calculate "Tissue specificity score" using JSD
... You're welcome! In the next few days I plan to release a new version with a CLI interface and a full tutorial explaining how to use the package inside Python. ...
written 12 months ago by elsoja110
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Answer: A: How to calculate "Tissue specificity score" using JSD
... In case you're still interested in that, I developed a Python package that computes several tissue-specificity metrics, including JSD. http://github.com/apcamargo/tspex I'm finishing a web version of it that will be online soon (I hope). ...
written 12 months ago by elsoja110
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Comment: C: How should a query a gene type in multiple genomes?
... I didn't know about RNA Central. I'll look into it right now. Thank you! As far as I know, it's not possible to query a specific gene type in Entrez, but I'll investigate it. ...
written 2.1 years ago by elsoja110
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Comment: C: How should a query a gene type in multiple genomes?
... The problem with `BiomaRt` is that I can only query one database (in this case, one genome) at a time. I suppose I could create a loop to automatequerying though multiple databases. ...
written 2.1 years ago by elsoja110
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How should a query a gene type in multiple genomes?
... I want to query all genes of a specific type (eg.: microRNAs) in genomes of multiple species. Initially I was doing this using Ensemble's BioMart, but it limits me to query a single genome at a time and I the web interface makes it impossible to automate the process. Is there a better way of doing t ...
search query written 2.1 years ago by elsoja110 • updated 2.1 years ago by genomax84k
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Answer: A: Transcripts with beta close to zero are considered differentially expressed in a
... This question was answered [here][1] [1]: https://github.com/pachterlab/sleuth/issues/140 ...
written 2.7 years ago by elsoja110
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Comment: C: Microbial diversity analysis using whole-genome metagenomic data
... Thank you. For what I've read, tools like CLARK, KRAKEN and Kaiju are the answer for my problem. ...
written 2.8 years ago by elsoja110
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Comment: C: Microbial diversity analysis using whole-genome metagenomic data
... Cross-posted on [StackExchange](https://bioinformatics.stackexchange.com/questions/2361/microbial-diversity-analysis-using-whole-genome-metagenomic-data) ...
written 2.8 years ago by elsoja110

Latest awards to elsoja

Great Question 7 weeks ago, created a question with more than 5,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 5 months ago, created a question with more than 1,000 views. For Transforming stranded RNA-Seq libraries in unstranded
Popular Question 10 months ago, created a question with more than 1,000 views. For Transforming stranded RNA-Seq libraries in unstranded
Popular Question 11 months ago, created a question with more than 1,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Microbial diversity analysis using whole-genome metagenomic data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Insert size in RNA-Seq library

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