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Hello,
I am excited to use the MicrobioStat package in order to test for differences in alpha diversity accross timepoints.
I have been working with phyloseq object so far and I would like to con…
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I am trying to run biobakery workflows (Python: 2.7.15; wgmx.py: v0.1) on a shared deployment (app tree) model.
When I run the following command locally:
``
INPUT=/mnt/efs/home/dmb6464/projects/s…
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An important question about random generator support remains in scikit-bio. I am pinging @wasade because this question also impacts biom-format, and I would like also to seek @mortonjt and @mataton 's…
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We will need a few sets of sequence data to work on in order to generate our data products.
We should aim to have a few taxonomic marker genes represented.
I can arrange some 16S/18S rRNA gene seq…
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there is some interest in translating between taxonomies (GTDB, NCBI, and maybe LINS), and this is something that we should be able to do somewhat straightforwardly in sourmash.
relevant issues -
…
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**Improvement Description**
I have reviewed the documentation and tutorial with an eye toward figuring out how a completely novice user (e.g., new microbiology grad student without any bioinformatics…
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hi there, I'm having an issue I hope you can help with. the checks were okay, but there is an error during the training process. I attached the log file,(let me know if you can access that alright). …
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Hello! I saw your recent preprint, "Scalable estimation of microbial co-occurrence networks with Variational Autoencoders" and I'm hopeful your method may solve my issues, but I wanted to touch base t…
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I recently started dipping my toes into published datasets from the Oxford Nanopore MinION sequencer. Their format is an hdf5 file, containing several types of metadata, "event data" (which is essenti…
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Hi @mikemc
Thanks for your email.
I am new to R and Phyloseq. However, I need to analyze the 16S rRNA data (please see the attached file for data format). I have the otu-tables & absolute abund…