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THE BIOBAKERY HELP FORUM

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WELCOME TO THE BIOBAKERY TOOLS AND TUTORIALS FORUM, WHICH PROVIDES SOFTWARE,
DOCUMENTATION, AND TUTORIALS FOR METHODS FOR MICROBIAL COMMUNITY PROFILING
DEVELOPED BY THE HUTTENHOWER LAB. MOST TOOLS ARE SUPPORTED BOTH AS INDIVIDUAL
SOFTWARE PACKAGES (TYPICALLY PYTHON OR R) AND WITHIN THE BIOBAKERY VIRTUAL
IMAGE, A PRE-BUILT PLATFORM THAT PROVIDES META’OMIC ANALYSIS TOOLS ALREADY
INSTALLED WITH DEPENDENCIES AND CONFIGURATION. FOR THE INTEGRATED BIOBAKERY
VIRTUAL ENVIRONMENT, PLEASE CLICK HERE.

Here are some tips for getting started:

 1. Feel free to browse existing questions and answers.
 2. To post a new question, please sign up / in using the buttons at the top
    right.
 3. For questions about a specific bioBakery tool (e.g. HUMAnN), please post to
    the corresponding category.
 4. For all other questions, please post to the “General Science” category.

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Category Topics
INFRASTRUCTURE AND UTILITIES

General bioBakery or infrastructure utilities for microbial community or other
computational biology research.
bioBakery workflows GraPhlAn KneadData AnADAMA2
3 / week

MICROBIAL COMMUNITY PROFILING

Tools for bioinformatics on raw microbial community data, typically quantifying
features such as taxa, genes, functions, metabolites, or other molecular or
cellular activities.
HUMAnN StrainPhlAn MetaPhlAn ShortBRED PanPhlAn PICRUSt PhyloPhlAn WAAFLE
MelonnPan MetaWIBELE PPANINI MACARRoN
7 / week

DOWNSTREAM ANALYSIS AND STATISTICS

Tools for microbial community modeling, significance calculations, differential
abundance testing, and more.
MaAsLin LEfSe MMUPHin HAllA SparseDOSSA CCREPE microPITA BAnOCC ARepA
6 / week

DATA RESOURCE

IBDMDB
1 / week

GENERAL MICROBIAL COMMUNITY SCIENCE AND ANALYSES

Questions not related to a specific tool, or dealing with general applications
or experimental design.
General microbial science and analysis
4

FEATURE/PULL REQUEST

Feature/Pull Request
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