User: elsoja

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elsoja30
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Posts by elsoja

<prev • 22 results • page 1 of 3 • next >
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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 7 days ago by elsoja30
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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 8 days ago by elsoja30
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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 13 months ago by elsoja30
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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 13 months ago by elsoja30
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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 13 months ago by elsoja30 • updated 13 months ago by genomax67k
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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 20 months ago by elsoja30
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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 21 months ago by elsoja30
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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 21 months ago by elsoja30
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Microbial diversity analysis using whole-genome metagenomic data
... I have data, obtained from a single metagenomic DNA sample, that consists of two MiSeq FASTQ files (R1 and R2) that I merged using [PEAR][1]. Now I want to estimate the abundances of the bacteria taxa to generate a figure like this one: [![enter image description here][2]][2] Figure from: *Panosy ...
mothur taxonomy metagenome qiime written 21 months ago by elsoja30 • updated 21 months ago by Brian Bushnell16k
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Comment: C: Transcripts with beta close to zero are considered differentially expressed in a
... I've done this already. Waiting for an answer. Thank you! https://groups.google.com/forum/#!topic/kallisto-sleuth-users/bRb4nRhoZZw ...
written 21 months ago by elsoja30

Latest awards to elsoja

Popular Question 12 months ago, created a question with more than 1,000 views. For Microbial diversity analysis using whole-genome metagenomic data
Popular Question 20 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 20 months ago, created a question with more than 1,000 views. For Insert size in RNA-Seq library

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