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pRoloc

A unifying bioinformatics framework for organelle proteomics

https://github.com/lgatto/proloc

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 13 DOI reference(s) in README
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
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    Committers with academic emails
    4 of 27 committers (14.8%) from academic institutions
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    Low similarity (17.1%) to scientific vocabulary

Keywords

bioconductor proteomics proteomics-data r spatial-proteomics visualisation

Keywords from Contributors

bioconductor-package mass-spectrometry metabolomics proteomexchange bioinformatics feature-detection peak-detection core-package rhdf5 hdf5
Last synced: 6 months ago · JSON representation

Repository

A unifying bioinformatics framework for organelle proteomics

Basic Info
Statistics
  • Stars: 16
  • Watchers: 4
  • Forks: 14
  • Open Issues: 18
  • Releases: 0
Topics
bioconductor proteomics proteomics-data r spatial-proteomics visualisation
Created over 13 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog

README.md

codecov.io

A unifying bioinformatics framework for spatial proteomics

The pRoloc suite set of software offers a complete software pipeline to analyse, visualise and interpret mass spectrometry-based spatial proteomics data such, for example, as LOPIT (Localization of Organelle Proteins by Isotope Tagging), PCP (Protein Correlation Profiling) or hyperLOPIT (hyperplexed LOPIT). The suite includes pRoloc, the mail software that focuses on data analysis using state-of-the-art machine learning, pRolocdata, that distributes numerous datasets, and pRolocGUI, that offers interactive visualisations dedicated to spatial proteomics. The software are distributed as part of the R/Bioconductor project.

Getting started

The pRoloc software comes with ample documentation. The main tutorial provides a broad overview of the package and its functionality. See the Articles tab for additional manuals.

pRolocGUI also offer several documentation files.

Here are a set of video tutorial that illustrate the pRoloc framework.

Help

Post your questions on the Bioconductor support site, tagging it with the package name pRoloc (the maintainer will automatically be notified by email). If you identify a bug or have a feature request, please open an issue on the github development page.

Installation

The preferred installation procedure uses the Bioconductor infrastructure:

```c

unless BiocManager is already installed

install.packages("BiocManager")

then

BiocManager::install("pRoloc") BiocManager::install("pRolocdata") BiocManager::install("pRolocGUI") ```

Pre-release/development version

The pre-release/development code on github can also be installed using BiocManager::install, as shown below. Note that this requires a working R build environment (i.e Rtools on Windows - see here). New pre-release features might not be documented not thoroughly tested and could substantially change prior to release. Use at your own risks.

```c

unless BiocManager is already installed

install.packages("BiocManager")

then, install from github

BiocManager::install("lgatto/pRoloc") BiocManager::install("lgatto/pRolocdata") BiocManager::install("lgatto/pRolocGUI") ```

References:

For refences about the software, how to use it and spatial proteomics data analysis:

  • Crook OM, Breckels LM, Lilley KS, Kirk PWD, Gatto L. A Bioconductor workflow for the Bayesian analysis of spatial proteomics [version 1; peer review: awaiting peer review]. F1000Research 2019, 8:446 (https://doi.org/10.12688/f1000research.18636.1)

  • Breckels LM, Mulvey CM, Lilley KS and Gatto L. A Bioconductor workflow for processing and analysing spatial proteomics data [version 2; peer review: 2 approved]. F1000Research 2018, 5:2926 (https://doi.org/10.12688/f1000research.10411.2)

  • Gatto L, Breckels LM, Burger T, Nightingale DJ, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS. A foundation for reliable spatial proteomics data analysis Mol Cell Proteomics. 2014 Aug;13(8):1937-52. doi: 10.1074/mcp.M113.036350. Epub 2014 May 20. PubMed PMID: 24846987

  • Gatto L, Breckels LM, Wieczorek S, Burger T, Lilley KS. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata Bioinformatics. 2014 May 1;30(9):1322-4. doi: 10.1093/bioinformatics/btu013. Epub 2014 Jan 11. PubMed PMID: 24413670.

Specific algorithms available in the software:

  • Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS, Trotter MW. The effect of organelle discovery upon sub-cellular protein localisation J Proteomics. 2013 Aug 2;88:129-40. doi: 10.1016/j.jprot.2013.02.019. Epub 2013 Mar 21. PubMed PMID: 23523639.

  • Breckels LM, Holden S, Wojnar D, Mulvey CMM, Christoforou A, Groen AJ, Kohlbacher O, Lilley KS and Gatto L. Learning from heterogeneous data sources: an application in spatial proteomics 2015 biorXiv, doi: http://dx.doi.org/10.1101/022152

  • Oliver M Crook, Claire M Mulvey, Paul D. W. Kirk, Kathryn S Lilley, Laurent Gatto A Bayesian Mixture Modelling Approach For Spatial Proteomics PLOS Computational Biology doi:10.1371/journal.pcbi.1006516

More resource

Contributing

Contributions to the package are more than welcome. If you want to contribute to this package, you should follow the same conventions as the rest of the functions whenever it makes sense to do so. Feel free to get in touch (preferable opening a github issue) to discuss any suggestions.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Owner

  • Name: Laurent Gatto
  • Login: lgatto
  • Kind: user
  • Location: Belgium
  • Company: de Duve Institute, UCLouvain

Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.

GitHub Events

Total
  • Issues event: 5
  • Watch event: 2
  • Delete event: 5
  • Issue comment event: 14
  • Push event: 30
  • Pull request event: 6
  • Create event: 5
Last Year
  • Issues event: 5
  • Watch event: 2
  • Delete event: 5
  • Issue comment event: 14
  • Push event: 30
  • Pull request event: 6
  • Create event: 5

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 2,012
  • Total Committers: 27
  • Avg Commits per committer: 74.519
  • Development Distribution Score (DDS): 0.654
Past Year
  • Commits: 56
  • Committers: 4
  • Avg Commits per committer: 14.0
  • Development Distribution Score (DDS): 0.429
Top Committers
Name Email Commits
Laurent l****0@c****k 697
Laurent l****o@g****m 493
l.gatto l****o@b****8 283
Laurent Gatto l****o@d****e 238
lmsimp l****p@g****m 119
Oliver M. Crook o****k@g****m 54
d.tenenbaum d****m@b****8 36
Dan Tenenbaum d****a@f****g 19
Nitesh Turaga n****a@g****m 14
J Wokaty j****y@s****u 10
Samuel Wieczorek s****k@c****r 9
Sebastian Gibb m****l@s****e 7
*tnaake* t****e@g****e 5
Herve Pages h****s@f****g 4
hpages@fhcrc.org h****s@f****g@b****8 4
mgerault 6****t 3
Charl-Hutchings c****1@c****k 3
Hervé Pagès h****s@f****g 2
vobencha v****a@g****m 2
vobencha v****n@r****g 2
s.arora s****a@b****8 2
lshep s****l@g****m 1
TomSmithCGAT t****8@c****k 1
Sonali Arora s****a@f****g 1
Marc Carlson m****n@f****g 1
m.carlson m****n@b****8 1
Kayla-Morrell k****l@r****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 5 cam.ac.uk: 3 roswellpark.org: 2 fredhutch.org: 1 gmx.de: 1 sebastiangibb.de: 1 cea.fr: 1 sph.cuny.edu: 1 dnavision.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 91
  • Total pull requests: 21
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 22 days
  • Total issue authors: 21
  • Total pull request authors: 7
  • Average comments per issue: 2.13
  • Average comments per pull request: 1.05
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 4
  • Average time to close issues: 21 days
  • Average time to close pull requests: about 1 month
  • Issue authors: 5
  • Pull request authors: 2
  • Average comments per issue: 2.86
  • Average comments per pull request: 0.25
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lgatto (43)
  • lmsimp (23)
  • ococrook (5)
  • Charl-Hutchings (2)
  • LiNk-NY (2)
  • kbarylyuk (1)
  • Tlicknack (1)
  • sgibb (1)
  • TomSmithCGAT (1)
  • ortizmateujuan (1)
  • nk448 (1)
  • ab604 (1)
  • OwenVennard (1)
  • LojzaZ (1)
  • daveshire (1)
Pull Request Authors
  • ococrook (8)
  • lmsimp (5)
  • sgibb (4)
  • Charl-Hutchings (2)
  • mgerault (2)
  • TomSmithCGAT (1)
  • lgatto (1)
Top Labels
Issue Labels
enhancement (9) bug (3)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 64,619 total
  • Total dependent packages: 3
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: pRoloc

A unifying bioinformatics framework for spatial proteomics

  • Versions: 7
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 64,619 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 5.2%
Downloads: 15.7%
Maintainers (1)
lms79@cam.ac.uk
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • BiocParallel * depends
  • MLInterfaces >= 1.67.10 depends
  • MSnbase >= 1.19.20 depends
  • R >= 3.5 depends
  • Rcpp >= 0.10.3 depends
  • methods * depends
  • Biobase * imports
  • BiocGenerics * imports
  • FNN * imports
  • LaplacesDemon * imports
  • MASS * imports
  • RColorBrewer * imports
  • biomaRt * imports
  • caret * imports
  • class * imports
  • coda * imports
  • dendextend * imports
  • e1071 * imports
  • ggplot2 * imports
  • grDevices * imports
  • graphics * imports
  • gtools * imports
  • hexbin * imports
  • kernlab * imports
  • knitr * imports
  • lattice * imports
  • mclust >= 4.3 imports
  • mixtools * imports
  • mvtnorm * imports
  • nnet * imports
  • plyr * imports
  • proxy * imports
  • randomForest * imports
  • sampling * imports
  • scales * imports
  • stats * imports
  • stats4 * imports
  • utils * imports
  • AnnotationDbi * suggests
  • BiocStyle >= 2.5.19 suggests
  • GO.db * suggests
  • Rtsne >= 0.13 suggests
  • akima * suggests
  • dplyr * suggests
  • fields * suggests
  • hpar >= 1.15.3 suggests
  • magick * suggests
  • nipals * suggests
  • pRolocdata >= 1.9.4 suggests
  • reshape * suggests
  • rgl * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests
  • vegan * suggests
  • xtable * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite