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bio-microbiome-differential-abundance

Reference examples tested with: DESeq2 1.42+, ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+ Before using code patterns, verify installed versions match. ...

by FreedomIntelligence

github 3 files

bio-microbiome-diversity-analysis

Reference examples tested with: R stats (base), ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+, vegan 2.6+ Before using code patterns, verify installed ve...

by FreedomIntelligence

github 3 files

bio-microbiome-qiime2-workflow

Reference examples tested with: DADA2 1.30+, MAFFT 7.520+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+ Before using code patterns,...

by FreedomIntelligence

github 3 files

bio-microbiome-taxonomy-assignment

Reference examples tested with: DADA2 1.30+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+ Before using code patterns, verify instal...

by FreedomIntelligence

github 3 files

bio-multi-omics-data-harmonization

Reference examples tested with: DESeq2 1.42+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pkg>...

by FreedomIntelligence

github 3 files

bio-multi-omics-mixomics-analysis

Reference examples tested with: mixOmics 6.26+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion("<pk...

by FreedomIntelligence

github 3 files

bio-multi-omics-mofa-integration

Reference examples tested with: scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pkg>...

by FreedomIntelligence

github 3 files

bio-multi-omics-similarity-network

Reference examples tested with: scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion('<pkg>...

by FreedomIntelligence

github 3 files

bio-pathway-go-enrichment

Reference examples tested with: R stats (base), clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ:...

by FreedomIntelligence

github 4 files

bio-pathway-kegg-pathways

Reference examples tested with: R stats (base), clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ:...

by FreedomIntelligence

github 4 files

bio-pathway-reactome

Reference examples tested with: R stats (base), ReactomePA 1.46+, clusterProfiler 4.10+ Before using code patterns, verify installed versions match. I...

by FreedomIntelligence

github 4 files

bio-pathway-wikipathways

Reference examples tested with: ReactomePA 1.46+, clusterProfiler 4.10+, rWikiPathways 1.24+ Before using code patterns, verify installed versions mat...

by FreedomIntelligence

github 4 files