songbird
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biocore
Vanilla regression methods for microbiome differential abundance analysis
Hi @mortonjt What format should I enter if I want to analyze SCFAs data in qiime? I tried to convert the form to biom and then to qza and encountered...
Are there plans to update songbird to work with latest and upcoming versions of Qiime2? This is a great tool. I can't always get it to work with my data...
From the readme of SongBird I can find that the X-axis of cv_error graph is the number of iterations. In the command this is defined by _"-epochs"_ argument. Though we...
I followed the installation instructions for creating a stand alone conda environment but was met with: ``` Traceback (most recent call last): File "/Users/dtmcdonald/miniconda3/envs/songbird_env/bin/songbird", line 8, in from songbird.multinomial import...
I'd like to try out songbird but I have a lot of data to prototype. Creating intermediate files really puts a bottleneck in my workflow and was wondering if I...
For datasets with >10k samples, the memory requirements can be quite high. If there isn't enough memory available, this can throw an out-of-memory error.
Hello! I ran songbird on my marine dataset and it seemed to have worked well for most variables. However, for the categorical variable, water mass, there are only output differential...
Hello, I am using Songbird stand alone, and it has worked perfectly until I ran into this issue using a very specific .biom file as input. This .biom file is...
Hi, I have a question about the input biom file. Regarding the interpretation of the results, does it make more sense to include the OTU table that includes all the...
How do you decide which taxa are reported in the differential ranking? Are the differentials that are reported the coefficients that are the most changing, or those that are significant,...
