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Create:
* tables for the GTDB basis
* tables with association with the classification of OTUs and ASVs in the platform
* functions for classification of representative sequences for OTUs and ASVs (…
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Processing the plaintext json that ASV produces every time the app starts up takes a long time (~2-3 minutes for pandas currently). We have the line
https://github.com/rhshadrach/asv-watcher/blob/f…
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Dear Benjamin
Thank you for developing this user-friendly R package for the challenge with contaminant filtration.
I have some questions about decontam below. I hope you have time for answering…
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When running on 16S data with prevalence and gtdb selected. Runs fine with UHGP
Quitting from lines 40-100 [setup] (phylogenize-report.Rmd)
Error in `pz.error()`:
! All trees had less than 2.5% o…
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The following section should be able to be modified to include the CFG$dada2_assignTaxonomy_nochim$refFasta in the filename, will be clunky with entire name (e.g. ASV_taxa_pr2_version_4.13.0_18S_dada2…
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Janet and others have expressed interest in having Hundo support denoising methods in addition to traditional OTU clustering.
This is something I'm interested in implementing, and I would appreciat…
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These are failing on an import from the compatibility module. Maybe you want to check this out for older versions.
```
[ 17.71%] · For sympy commit hash 232be474:
[ 17.71%] ·· Building for py2.7-fast…
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## What is the proposed Cheat Sheet about?
As suggested by my conversations with the OWASP ASVS leaders, my proposals for ASVS requirements were too detailed (as they were taken straight from the off…
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PEM-- updated
9 years ago
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Hello,
I have to plot a histogram of the relative abundance of the different ASVs, and based on this suggest a cutoff for removing low abundance ASVs.
How can I plot the relative abundance of ASVs a…