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.
A curated R script is available with the detailed instructions to analyse intestinal microbiota.
The required files to use the package are :
The next columns should contain the peptide abundances as spectral counts. The name of the columns should be identical to the content of the column msrunfile from the metadata information.
List of protein names associated to the identified peptides. This file should have eight columns named:
SubGroup count: number of subgroups (also known as metaproteins) per group
Metadata information. At least three columns must be present and named as:
Additional columns containing complementary information can be added by the user (ex. replicates, order of injection, etc.). The separation between columns should be indicated by tabulation
Catalog of genes with taxonomic annotations with the following format:
A column named species.genus.family.order.class.phylum.superkingdom. The taxonomic classification can be obtained from a tool of sequences aligment and must be ordered by species, genus, family, order, class, phylum and superkingdom. The characters inside must be concatenated by a comma (ex."Streptococcus anginosus,Streptococcus,Streptococcaceae,Lactobacillales,Bacilli,Firmicutes,Bacteria"). For the application case you can download the Integrated non-redundant Gene Catalog (IGC) 9.9 database.
Functional annotations of genes (optional). The functional annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were added to the IGC 9.9 database. . This file should include two columns named:
Everybody is welcome to contribute to the metaprotr.
If you found an error please describe it in the issues section and address it to the package mantainer.
Please provide the following information: * Summarize the bug encountered concisely. * What is the current bug behavior? * What is the expected correct behavior? * Describe the steps to reproduce it. * Paste logs and/or screenshots. * Add possible fixes.
To improve, modify or add a new feature/function to the project please follow this procedure:
Create a new branch from "stable" and name it with the feature/function that you will work on.
Make changes and commits to this branch while developing.
When making commits it is recommended to use the following graphical identifiers:
| Identifier | Code | Description | |-----------------------|------------------------:|----------------:| | :lollipop: | : lollipop : | Minor change (ex. comment, renaming) | | :pencil2: | : pencil2 : | New code | | :wrench: | : wrench : | Code refactoring | | :checkered_flag: | : checkered_flag : | code test, check or verification | | :bug: | : bug : | bug detected |
git commit -m ':pencil2: writing core logic of an awesome function'
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