Open fischer-hub opened 2 years ago
fischer-hub
commented
2 years ago humann3.0 samples, these are relatively small and should contain genes to some degree since they are from the humann3.0 tutorial, however these are fasta files and i think they are preprocessed as well..
EDIT: also no biological/experimental replicates per sample, so no analysis with DESeq2/edgeR possible
fischer-hub
commented
2 years ago Intestinal response to prenatal inflammation (sus scrofa) 40 samples!! But theres also a text file containing the normalized counts so maybe a good catch!
Enhanced metabolic potentials and functional gene interactions of microbial stress response towards high elevation in freshwater lakes 6 samples per lake, 4 lakes, 2 HEL and 2 LEL -> 24 samples in total but small file size. Note that we dont need host sequence removal for this one.
fischer-hub
commented
2 years ago metagenomic wgs data from human urine samples, 10 samples with lots of metadata available, good for analysis
fischer-hub
commented
2 years ago The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants
about 150 samples, WGS data, uses humann3, however only one contrast had significant results and MAaslin2 was only used for pathway abundance, gene abundance was tested with willcoxon test only
fischer-hub
commented
2 years ago The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants
about 150 samples, WGS data, uses humann3, however only one contrast had significant results and MAaslin2 was only used for pathway abundance, gene abundance was tested with willcoxon test only
This is unpublished data.
Would be nice to have some test data that is not to big to reduce runtime but where we know what the expected result is. Even more important when it comes to the statistical analysis!!