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In this manuscript DAA methods have been benchmarked and a new method was proposed: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01320-0 we should check if any of these meth…
mlist updated
1 month ago
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Dear
Is there a way to link the results of each biomarker resulting from the Lefse, ancombc, metagenomeSeq and Aldex2 analyses?
I was doing an analysis of all of them and I see that some of them co…
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After talking to @qiyunzhu , it is becoming clear that skbio would need to have a differential abundance method that can at least provide directionality (i.e. features increase / decrease in abundance…
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Hello, a newbie summer intern here, wanted some advice!!
While I was making some grammatical and technical edits to the differential data analysis(DAA) chapter, I was wondering how it will be like …
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Dear Chi,
I am having some trouble interpreting the LEfSe results from my dataset, and was wondering if there could be a calculation error when obtaining the LDA scores. The distribution of certai…
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Hello team
I would like to split my dataset by condition and annotate the cell types using SingleR. Is there a way to visualize or compare the differences in cell type annotations between the two con…
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## Request
I would like to propose support for sample-/gene-dependent normalization factors to enable the use length offset matrices from [pytximport](https://pytximport.readthedocs.io/en/latest/st…
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Dear Caffery Yang,
I followed the directions described in the workflow, but I got errors for both ALDEx2 and LinDA methods. My metadata file is as follow:
sample-id mat-colour year …
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Hi,
Thank you for an excellent approach to functional metagenomics. I have a major concern with the normalization method based on relative abundance. It has been demonstrated that is one of the wor…
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Hello, I'm new to picrust2 output analysis and I'm having an error when performing pathwat_daa function with the EC pathway workflow.
This is the code I ran:
# Workflow for MetaCyc Pathway and EC
…