species_fw

Data containing the abundance of 17 species 
 expressed in spectral counts. Data generated from an Orbitrap 
 Fusion Lumos Tribrid Mass Spectrometer. The dataset contains 
 the metaproteomes from three extraction methods: i) "Q" for Qiagen, 
 ii) "FW" for fecal waters, and iii) "Q_FW" for the mixture 
 of Qiagen and fecal waters. Data generated in the context of 
 the project Microbiome Rapid Access (Universit&lt;U+00E9&gt; Paris-Saclay).

datasets


Set of tools for descriptive analysis of metaproteomics data generated from high-throughput
mass spectrometry instruments. These tools allow to cluster peptides and proteins abundance,
expressed as spectral counts, and to manipulate them in groups of metaproteins. This information
can be represented using multiple visualization functions to portray the global metaproteome
landscape and to differentiate samples or conditions, in terms of abundance of metaproteins,
taxonomic levels and/or functional annotation. The provided tools allow to implement flexible
analytical pipelines that can be easily applied to studies interested in metaproteomics analysis.

Aaron Millan-Oropeza

metaprotr

Metaproteomics Post-Processing Analysis

Catherine Juste

Ariane Bassignani

C<c3><a9>line Henry

species_fw function

A list of four elements defined as "spectral_count_object" with 
 taxonomic annotation generated with the function "crumble_taxonomy"<dl class="dl-horizontal">
 <dt>SC_subgroups</dt><dd>dataframe with 9 samples containing 17 
 especies with abundance expressed as spectral counts</dd>
 <dt>metadata</dt><dd>information related to the 9 samples from the 
 experiment</dd>
 <dt>peptides_proteins</dt><dd>information related to each of the 
 1557 identified peptides</dd>
 <dt>type_object</dt><dd>character indicating the type of object</dd>
 </dl>

Format

species_fw — species_fw

A list of four elements defined as "spectral_count_object" with 
 taxonomic annotation generated with the function "crumble_taxonomy"<dl class='dl-horizontal'>
 <dt>SC_subgroups</dt><dd>dataframe with 9 samples containing 17 
 especies with abundance expressed as spectral counts</dd>
 <dt>metadata</dt><dd>information related to the 9 samples from the 
 experiment</dd>
 <dt>peptides_proteins</dt><dd>information related to each of the 
 1557 identified peptides</dd>
 <dt>type_object</dt><dd>character indicating the type of object</dd>
 </dl>

species_fw: species_fw

Description

Usage

Arguments

Format