pitagora-network.github.io

Huttenhower Labは、メタゲノム・機能ゲノム解析のためのGalaxyサーバー。

http://huttenhower.org/galaxy/ https://huttenhower.sph.harvard.edu/galaxy/

Huttenhower Lab Tools

Composition Analysis

Statistical Analysis

Segata Lab - Computational Metagenomics

MetaPhlAn2 tutorial | Visualize results | Create a cladogram with GraPhlAn

MetaPhlAn2は、メタゲノム配列データから微生物群集の組成を推定する。

biobakery / MetaPhlAn2 — Bitbucket

GraPhlAn in Galaxy

PhyloPhlAn Tutorial | 1.2 Visualization with GraPhlAn (Galaxy module)

PhyloPhlAnは、全ゲノム配列情報に基づいて系統樹を再構築する。

You may use tree visualization softwares to inspect the files. We provide support for GraPhlAn to visualize the output tree. Please follow the instructions below to view the resulting tree. Go to the Huttenhower Galaxy Server. Click on the GraPhlAn link on the left pane. Click on the Load input tree link on the left pane under the GraPhlAn link, and upload the PhyloXML file (for this tutorial example_corynebacteria.tree.reroot.xml). You can do this by clicking on the Browse button, selecting the PhyloXML file, and then pressing the Execute button.

https://bitbucket.org/repo/49y6o9/images/3667087422-phylophlan1.png

PICRUSt

PICRUStは、（16S rRNA等）マーカー遺伝子の調査と完全ゲノムからメタゲノムの機能を予測する。

[Installing PICRUSt in Galaxy https://github.com/picrust/picrust_galaxy]

MetaPhlAn (Galaxy Module)

MetaPhlAnは、メタゲノム配列データから微生物群集の組成を推定する。

https://bitbucket.org/repo/49y6o9/images/1284509036-metaphlan2_out.png

MetaPhlAn Visualization | Using the GraPhlAn Galaxy module

??????????

  1. Issue # It is stated that ‘• Select the input tree file (merged_table.tree. for this tutorial)’ at https://bitbucket.org/biobakery/biobakery/wiki/metaphlan#rst-header-using-the-graphlan-galaxy-module

However, the input tree file “merged_table.tree” was not found….. Also, the filename is “tmp.tree” at https://bitbucket.org/repo/49y6o9/images/3445894745-graphlan_load.png ??????????

GraPhlAn (Galaxy module)

GraPhlAnは、分類学的・系統学的ツリーを環状で表現する。

以下のデモ用ファイルをダウンロードする:

GraPhlAn Galaxyを使用する手順は以下の通り

ステップ1: Huttenhower Galaxy serverに行く。

ステップ2: ツリー・ファイルをアップロード

https://bitbucket.org/repo/49y6o9/images/4218449326-Screenshot%20from%202016-07-11%2015-06-50.png

ステップ3: ツリーに注釈を付ける。

https://bitbucket.org/repo/49y6o9/images/1693804870-Screenshot%20from%202016-07-11%2015-24-32.png

ステップ4: 注釈ファイルをアップロード

https://bitbucket.org/repo/49y6o9/images/2026880093-Screenshot%20from%202016-07-11%2015-38-52.png

ステップ5: ツリーにリングを追加

https://bitbucket.org/repo/49y6o9/images/1582742557-Screenshot%20from%202016-07-11%2015-46-15.png

ステップ6: ツリーをプロット

https://bitbucket.org/repo/49y6o9/images/3764378899-Screenshot%20from%202016-07-11%2015-59-10.png

結果として得られる画像を以下に示す:

https://bitbucket.org/repo/49y6o9/images/510538251-Screenshot%20from%202016-07-11%2016-06-39.png

GraPhlAnの他のオプションについては、GraPhlAnのドキュメントを参照されたい。

LEfSe (Galaxy)

LEfSe (Linear discriminant analysis Effect Size) は、クラス間の違いを説明する可能性が最も高い 特徴（生物、クレード、OTU、遺伝子、機能）を決定する。

http://huttenhower.sph.harvard.edu/webfm_send/129

??????????

  1. Issue # It is stated that “click on the LEfSe link on the left pane” and “Click on the Load data link to upload the input file” at https://bitbucket.org/biobakery/biobakery/wiki/lefse#rst-header-lefse-galaxy

However, [LEfSe] -> [Load data] was not found at http://huttenhower.sph.harvard.edu/galaxy ??????????

https://bitbucket.org/repo/49y6o9/images/3931070337-load_lefse_graphlan.png

[Meta’omic taxonomic profiling with MetaPhlAn2 and biomarker discovery with LEfSe Curtis Huttenhower 08-15-14](https://stamps.mbl.edu/images/c/c2/Stamps02-lab1-pdf.pdf)
[Meta’omic Analysis with MetaPhlAn & LEfSe Eric Franzosa 17 February 2013](http://www.cs.utexas.edu/users/tandy/franzosa-workshop.pdf)

MaAsLin (Galaxy module)

MaAsLinは、臨床メタデータと実験データとの間の関連を発見する。

MaAsLin requires an input file of microbial abundance table with metadata attached (e.g.: sample input). Go to the Huttenhower Galaxy server. Click on the MaAsLin link on the left pane, and then on the Load data for MaAsLin link. Click on the Choose File button to select the input file (microbial abundance table with metadata data attached) OR enter the URL in the URL/Text text box to upload the data. Click on the Execute button.

microPITA (Galaxy module)

microPITA (microbiomes: Picking Interesting Taxonomic Abundance) は、2段階（階層）の研究でサンプルの選択を可能にする。

  1. microPITA (Galaxy module) microPITA requires a PCL or BIOM input file. For further information on details of format, please refer to the documentation. For the purpose of this tutorial we will be using a sample input file depicting the general format of the input file. Go to the Huttenhower Galaxy server. Click on the microPITA link on the left pane, and then on the Load data for microPITA link. Click on the Choose File button to select the input file OR enter the URL in the URL/Text text box to upload the data. Click on the Execute button.

SparseDOSSA Galaxy

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