README.md
In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines
RomicsProcessor
RomicsProcessor is an R package that can be used to analyze omics data.
The package provides a structured R object to store the data, allowing for reproducible
data analysis. The package also supports creating analytical pipelines from
previously processed objects and applying these pipeline to other objects.
This allows for rapid development and reuse of bioinformatics methods.
Installation
To install the package in R please first make sure devtools is installed
install.packages("devtools")
When devtools is installed, run the following command to install RomicsProcessor and its dependencies
devtools::install_github("PNNL-Comp-Mass-Spec/RomicsProcessor")
Alternately, download the
built package
and install the package manually.
We recommend the installation of the Bioconductor package 'sva' if batch corrections are needed and of 'pmartR'.
Example of use
The folder /Example contain an
R markdown file
.
This example consist in an analysis of the proteome of B. cereus grown in different media.
The Raw LC-MS/MS data is publicly available, on MassIVE, FTP at the following address (ftp://massive.ucsd.edu/MSV000085696/).
It was analyzed using MaxQuant set with the
attached parameters
.
The MaxQuant output
proteinGroups.txt
Can be used as data and the
metadata
is also provided.
The different examples dataset are accessible directly inside the package
data folder.
Cite the code
To cite the package please use the following DOI:
Contacts
Written by @GeremyClair for the Department of Energy (PNNL, Richland, WA) \
E-mail: geremy.clair@pnnl.gov or proteomics@pnnl.gov \
Website: https://omics.pnl.gov/ or https://panomics.pnnl.gov/
License
RomicsProcessor is licensed under the 2-Clause BSD License;
you may not use this file except in compliance with the License. You may obtain
a copy of the License at https://opensource.org/licenses/BSD-2-Clause
Copyright 2019 Battelle Memorial Institute
PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
RomicsProcessor
RomicsProcessor is an R package that can be used to analyze omics data. The package provides a structured R object to store the data, allowing for reproducible data analysis. The package also supports creating analytical pipelines from previously processed objects and applying these pipeline to other objects. This allows for rapid development and reuse of bioinformatics methods.
Installation
To install the package in R please first make sure devtools is installed
install.packages("devtools")
When devtools is installed, run the following command to install RomicsProcessor and its dependencies
devtools::install_github("PNNL-Comp-Mass-Spec/RomicsProcessor")
Alternately, download the built package and install the package manually.
We recommend the installation of the Bioconductor package 'sva' if batch corrections are needed and of 'pmartR'.
Example of use
The folder /Example contain an R markdown file .
This example consist in an analysis of the proteome of B. cereus grown in different media. The Raw LC-MS/MS data is publicly available, on MassIVE, FTP at the following address (ftp://massive.ucsd.edu/MSV000085696/).
It was analyzed using MaxQuant set with the attached parameters .
The MaxQuant output proteinGroups.txt Can be used as data and the metadata is also provided.
The different examples dataset are accessible directly inside the package data folder.
Cite the code
To cite the package please use the following DOI:
Contacts
Written by @GeremyClair for the Department of Energy (PNNL, Richland, WA) \ E-mail: geremy.clair@pnnl.gov or proteomics@pnnl.gov \ Website: https://omics.pnl.gov/ or https://panomics.pnnl.gov/
License
RomicsProcessor is licensed under the 2-Clause BSD License; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause
Copyright 2019 Battelle Memorial Institute
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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