gemelli
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biocore
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse...
https://github.com/cameronmartino/gemelli/blob/9976f4e7634c269b9f7b8b243064a98996d61d35/.travis.yml#L5-L6 These lines specify that python 3.5 should be used but this line: https://github.com/cameronmartino/gemelli/blob/9976f4e7634c269b9f7b8b243064a98996d61d35/.travis.yml#L17 Will update python to 3.6.7
Using qiime2-amplicon-2024.2 with CLI qc-rarefy errored on the first sample that is in the unrarefied and not in the rarefied dataset Code: ``` qiime gemelli rpca \ --i-table ../data/core_diversity_healthy_r11800/rarefied_table.qza \...
I am unable to run Gemelli with QIIME 2 2023.7 due to a disagreement between the "int" type in numpy 1.24.4 and gemelli 0.0.9; error message below: Do you have...
computation with active SVD works like a charm ``` (qiime2-amplicon-2023.9) rs500-bcf-01 x86_64 ~/MicrobiomeAnalyses/Projects/Pandyra_CBP_Mb1-Cre>qiime gemelli tempted-factorize --i-table tempted_counts_CBP_clr.qza --m-sample-metadata-file tempted_meta_CBP.tsv --p-individual-id-column 'host_subject_id' --p-state-column 'timepoint' --output-dir ./gemelli_CBP_noSVD/ --p-n-components 7 --p-svd-centralized Saved PCoAResults...
For the python input it would be great if a simple pandas table or numpy array could be used as input.
Is there a way to easily tie which feature came from which modality at the moment? As far as I can tell, the current implementation stores all features across tables...
Using simulated random data I get the ``` gemelli/gemelli/preprocessing.py:426: RuntimeWarning: divide by zero encountered in log mat = np.log(matrix_closure(mat)) ``` _Originally posted by @SilasK in https://github.com/biocore/gemelli/issues/75#issuecomment-1864115649_
Working on doing CTF using the qiime2 CLI, but got an error I don't quite understand. ``` !qiime gemelli ctf \ --i-table ../data/Microbiome/pool_filtered/RPCA/gemelli_filtered.qza \ --m-sample-metadata-file ../data/Microbiome/14577_fixed.txt \ --m-feature-metadata-file ../../shotgun_scripts/woltka_v2_taxonomy.qza \...