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PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States — PICRUSt 1.0.0-dev documentation

PICRUSt 1.0.0-dev documentation. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. Enter search terms or a module, class or function name. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. PICRUSt is freely available under the GPL. Langille, M....

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PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States — PICRUSt 1.0.0-dev documentation | picrust.github.io Reviews

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PICRUSt 1.0.0-dev documentation. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. Enter search terms or a module, class or function name. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. PICRUSt is freely available under the GPL. Langille, M&#46...

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PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States — PICRUSt 1.0.0-dev documentation | picrust.github.io Reviews

https://picrust.github.io

PICRUSt 1.0.0-dev documentation. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. Enter search terms or a module, class or function name. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. PICRUSt is freely available under the GPL. Langille, M&#46...

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Citing PICRUSt — PICRUSt 1.1.0 documentation

http://picrust.github.io/picrust/citing_picrust.html

PICRUSt 1.1.0 documentation. Citing ancestral state reconstruction algorithms used by PICRUSt. Citing tools used to generate your OTU table. On this page we’ve compiled both the PICRUSt citation and links to several tools that PICRUSt is built on to make citing these various software packages easier. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. The manuscript describing PICRUSt can be found here. APE: Analyses of phylogenetics and evolution in R language.

2

News & Announcements — PICRUSt 1.1.0 documentation

http://picrust.github.io/picrust/news.html

PICRUSt 1.1.0 documentation. 10-12-16: Official release of PICRUSt 1.1.0. 09-03-13: Official release of PICRUSt 1.0.0. 08-25-13: PICRUSt published in Nature Biotechnology. 07-10-13: PICRUSt presented by Morgan Langille at Gordon Research Conference: Applied and Environmental Micobiology. 02-22-13: PICRUSt now available in Galaxy. 02-13-13: PICRUSt presented by Curtis Huttenhower at Keystone Symposia: The Gut Microbiome. And the Symposium and Workshop on New Methods for Phylogenomics and Metagenomics.

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PICRUSt Methods — PICRUSt 1.1.0 documentation

http://picrust.github.io/picrust/methods/index.html

PICRUSt 1.1.0 documentation. Constructing PICRUSt reference OTU collection. PICRUSt 1.1.0 documentation.

4

How PICRUSt Works — PICRUSt 1.1.0 documentation

http://picrust.github.io/picrust/tutorials/algorithm_description.html

PICRUSt 1.1.0 documentation. 1 Tree Pruning and Formatting. 2 Ancestral State Reconstruction. 16S rRNA Copy Number Prediction. For an alternative presentation of the same algorithm, along with controls please see the PICRUSt paper. These gene content predictions are precalculated for protein-coding genes present in KEGG or COG gene families and 16S rRNA gene copy number. Therefore users do not typically need to recalculate the gene content predictions to use PICRUSt. For details on the file format). ...

5

Metagenome Prediction Tutorial — PICRUSt 1.1.0 documentation

http://picrust.github.io/picrust/tutorials/metagenome_prediction.html

PICRUSt 1.1.0 documentation. Step 1: Normalize OTU Table. Step 2: Predict Functions For Metagenome. Step 3: Analysing Predicted Metagenomes. This tutorial explains how to predict a microbial community metagenome using PICRUST, based on 16S (or other marker gene) data as detailed in Picking OTUs for use in PICRUSt. Please note that PICRUSt by default uses the relatively new biom. Format for representing OTU tables and Gene tables (e.g. KOs by samples). This has several benefits. Step 1: Normalize OTU Table.

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Developing computational methods to better understand the microbial world. Since we’re a lab focused on the computational side of biology, we have several bioinformatics software packages that we’ve either developed directly in our lab or in conjunction with other bioinformatics labs. Cology) is an open source software package for the comparison and analysis of microbial communities, taking users from their raw sequencing data through publication-quality graphics. The BIOM Format ( BI.

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Bowman Lab: Marine microbial ecology. Tutorial: Analysis with paprica. Tutorial: Building the paprica database →. Correctly evaluating metabolic inference methods. March 4, 2016. Last week I gave a talk at the biennial Ocean Sciences Meeting that included some results from analysis with paprica. Spearman’s correlation between predicted and observed enzyme abundance in four marine metagenomes. The correlation looks decent, right? After the talk I was approached by a well known microbial ecologist who sugg...

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PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States — PICRUSt 1.0.0-dev documentation

PICRUSt 1.0.0-dev documentation. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. Enter search terms or a module, class or function name. PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. PICRUSt is freely available under the GPL. Langille, M&#46...

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