songbird
songbird copied to clipboard
biocore
Vanilla regression methods for microbiome differential abundance analysis
At the moment, tensorboard is disabled when running the qiime2 songbird command. The original motivation was because an additional logging directory needs to be created in order to enable this....
Right now, we can install songbird via pip, but it'll require numpy and biom-format to be installed before hand. One way to do this is to create a conda environment...
Hi, I'm on a mac and when I ran the command `qiime songbird multinomial --i-table redsea.biom.qza --m-metadata-file data/redsea/redsea_metadata.txt --p-formula "Depth+Temperature+Salinity+Oxygen+Fluorescence+Nitrate" --o-differentials differentials.qza --o-regression-stats regression-stats.qza --o-regression-biplot regression-biplot.qza --verbose` I got this...
We definitely don't need - `sklearn` - `seaborn` - `ipython` Need to trim before version 1.0 Also python3.7 is breaking for some reason ...
Standalone Songbird doesn't understand these rows, so it'll interpret them as actual samples (messing things up slightly). This is already documented in the README, but it'd be good to automatically...
As discussed in #70 , we don't want to arbitrary save logging information in a default location (esp if it is running in qiita or something). Having a `--p-logging-dir` option...
@vjcantu and I ran into this today -- if values in this column are labelled e.g. `train` and `test`, then 0 `Train` samples are identified (see line 189 below) and...