| title | author |
|---|---|
My R packages |
Laurent Gatto |
Latest udate: Mon Apr 9 16:05:15 2018
This post provides a short summary of some packages I develop, maintain or actively contribute to. Some packages are quite mature, other early stages. The final table provides the package version in the respective repositories. For an up-to-date version of this document, see https://lgatto.github.io/my-r-packages/.
This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics.
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.
The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny.
Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015.
The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.
The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.
The hpar package provides a simple R interface to and data from the Human Protein Atlas project.
A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.
These recipes convert a variety and a growing number of public proteomics data sets into easily-used standard Bioconductor data structures.
The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.
The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.
Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument.
S4 generic functions needed by Bioconductor proteomics packages.
Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
Educational package used in R courses to illustrate object-oriented programming and package development. Using biological sequences (DNA and RNA) as a working example.
The package provides utiliites to detrieve and inspect the download stats for any Bioconductor package and to calculate and visualise dependencies between packages.
A simple and consistent interfaces to various tasks involving the Gene Ontology and Ontology terms manipulation.
(release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel) (release) (devel)| package | repository | GitHub | ||
|---|---|---|---|---|
| RforProteomics | Bioconductor | 1.15.0 | 1.17.1 | 1.17.1 |
| mzR | Bioconductor | 2.12.0 | 2.13.6 | 2.13.6 |
| MSnbase | Bioconductor | 2.4.2 | 2.5.10 | 2.5.11 |
| pRoloc | Bioconductor | 1.18.0 | 1.19.3 | 1.19.4 |
| pRolocGUI | Bioconductor | 1.12.0 | 1.13.1 | 1.13.1 |
| pRolocdata | Bioconductor | 1.16.0 | 1.17.3 | 1.17.3 |
| rols | Bioconductor | 2.6.1 | 2.7.2 | 2.7.2 |
| rpx | Bioconductor | 1.14.0 | 1.15.0 | 1.13.5 |
| hpar | Bioconductor | 1.20.0 | 1.21.1 | 1.21.1 |
| Pbase | Bioconductor | 0.18.0 | 0.19.1 | 0.15.3 |
| ProteomicsAnnotationHubData | Bioconductor | 1.8.0 | 1.9.0 | 1.3.3 |
| qcmetrics | Bioconductor | 1.16.0 | 1.17.1 | 1.17.1 |
| synapter | Bioconductor | 2.2.0 | 2.3.1 | 2.3.2 |
| synapterdata | Bioconductor | 1.16.0 | 1.17.0 | Not available on Github |
| ProtGenerics | Bioconductor | 1.10.0 | 1.11.0 | 1.9.1 |
| yaqcaffy | Bioconductor | 1.38.0 | 1.39.0 | Not available on Github |
| sequences | CRAN 0.5.9 | 0.5.11 | ||
| biocpkgs | Not in any package repository | 0.1.2 | ||
| yagop | Not in any package repository | 0.1.0 |