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The package description states that a feature of the package is to subset a biom file. Does this include subsetting the entire biom by samples and/or observations or just subsetting the OTU table, tax…
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I am trying to use msa package to create tree as described in Bioconductor workflow for microbiome data analysis: Ben J. Callahan , Kris Sankaran , Julia A. Fukuyama , Paul J. McMurdie ,
Susan P. Ho…
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HI I am trying to run "mergePairsByID" in dada2, however I get the error message: could not find function "mergePairsByID". Dada2 is updated, library loaded, etc..
When I check the dada2 active funct…
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Dear developer,
When I use kv_import.py to import genbank files, a lot warnings output as blow:
`WARNING:root:No locus_tag found for feature - this will cause issues`
Are there any serious co…
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Hello,
As a school project, I am developing a Qiime User Interface in JAVA for Windows using SSH to access a virtualbox and run the scripts for Qiime. This is currently for personal (educational) …
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The core microbiome functions depend on functions in https://github.com/microbiome/microbiome, which introduces a lot of additional dependencies.
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I'd like to start a discussion on how to implement management of growth media. I can think of two approaches:
1. Add a new method to cobra.Model that takes either a dictionary or a json file with the …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/mani2012/PathoStat
Confirm the following by editing eac…
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Hi,
I'm novice user of QIIME, which is using pycogent version 1.5.3, and I get an exception in DenseAlignment **init**(). After starting up the debugger the error is with the type conversion:
p( typ…