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biotapy

Getting started

  • Tutorials
    • Getting started
    • Quick tour
    • The phyloseq analysis vignette in biotapy
    • Function in an IBD cohort

User guide

  • Guide
    • Data model
    • Reading and writing data
    • Example datasets
    • Transforms
    • Aggregation
    • Function
    • Filtering and rarefaction
    • Diversity
    • Ordination and PERMANOVA
    • Plotting
  • Coming from R

API reference

  • API
    • biotapy.io.read_biom
    • biotapy.io.read_dada2
    • biotapy.io.read_humann
    • biotapy.io.read_metaphlan
    • biotapy.io.read_phyloseq
    • biotapy.io.read_picrust2
    • biotapy.io.read_picrust2_traits
    • biotapy.io.read_qiime2
    • biotapy.io.write_biom
    • biotapy.datasets.enterotype
    • biotapy.datasets.enzyme
    • biotapy.datasets.esophagus
    • biotapy.datasets.global_patterns
    • biotapy.datasets.hmp2
    • biotapy.datasets.toy
    • biotapy.datasets.toy_humann
    • biotapy.pp.filter_features
    • biotapy.pp.filter_samples
    • biotapy.pp.rarefy
    • biotapy.pp.relative
    • biotapy.pp.tax_glom
    • biotapy.fn.contributions
    • biotapy.fn.func_glom
    • biotapy.fn.functional_redundancy
    • biotapy.fn.load_hierarchy
    • biotapy.fn.renorm
    • biotapy.tl.alpha
    • biotapy.tl.beta
    • biotapy.tl.nmds
    • biotapy.tl.pcoa
    • biotapy.tl.permanova
    • biotapy.tl.unifrac
    • biotapy.pl.bar
    • biotapy.pl.contributions
    • biotapy.pl.heatmap
    • biotapy.pl.ordination
    • biotapy.pl.richness
    • biotapy.pl.scree

Project

  • Design
  • Performance
  • Contributing guide
  • Changelog
  • References
  • Repository
  • Suggest edit
  • Open issue
  • .md

Tutorials

Tutorials#

  • Getting started
  • Quick tour
  • The phyloseq analysis vignette in biotapy
  • Function in an IBD cohort

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By Pedro Ribeiro

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