peakPantheR

On-instrument and post-acquisition targeted feature extraction

https://github.com/phenomecentre/peakpanther

Science Score: 20.0%

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
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DOI references
✓
Academic publication links
Links to: zenodo.org
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Committers with academic emails
3 of 8 committers (37.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.2%) to scientific vocabulary

Keywords

feature-detection mass-spectrometry metabolomics

Keywords from Contributors

bioconductor-packages gene ontologies sequencing immune-repertoire grna-sequence proteomics count phylogenetic-profile dna-methylation

Last synced: 10 months ago · JSON representation

Repository

On-instrument and post-acquisition targeted feature extraction

Basic Info

Host: GitHub
Owner: phenomecentre
Language: R
Default Branch: devel
Homepage:
Size: 4.51 MB

Statistics

Stars: 12
Watchers: 6
Forks: 1
Open Issues: 3
Releases: 11

Topics

feature-detection mass-spectrometry metabolomics

Created over 8 years ago · Last pushed about 2 years ago

Metadata Files

Readme

README.md

peakPantheR

Package for Peak Picking and ANnoTation of High resolution Experiments in R, implemented in R and Shiny

Overview

peakPantheR is an R/Bioconductor package that implements functions to detect, integrate and report pre-defined features in MS files (e.g. compounds, fragments, adducts, …). It is designed for:

Real time feature detection and integration (see Real Time Annotation)
- process multiple compounds in one file at a time
Post-acquisition feature detection, integration and reporting (see Parallel Annotation)
- process multiple compounds in multiple files in parallel, store results in a single object

peakPantheR can process LC/MS data files in NetCDF, mzML/mzXML and mzData format as data import is achieved using Bioconductor’s mzR package.

The reference versions of peakPantheR is available on the corresponding Bioconductor page (release or dev version).

Active development and issue tracking take place on the github page, while an overview of the package, vignettes and documentation are available on the supporting website.

Installation

To install peakPantheR: r install.packages("BiocManager") BiocManager::install("peakPantheR")

To install the development version from GitHub: r BiocManager::install("phenomecentre/peakPantheR")

Usage

Both real time and parallel compound integration require a common set of information:

Path(s) to netCDF / mzML MS file(s)
An expected region of interest (RT / m/z window) for each compound.

Vignettes

An overview of the package and detailed information on usage are available in the following vignettes:

Examples

Besides the vignettes, more tutorials are available via github:

Targeted integration of metabolites from 3 LC-MS profiling dataset using peakPantheR: Application of peakpPantheR to extract features from 3 LC-MS assays from a human urine metabolic profiling study on cognitive decline and dementia.
Quality-Control of peakPantheR extracted using the nPYc-Toolbox: Tutorial on how to use the nPYC-Toolbox to perform QC on peakPanther extracted datasets.

Contributing

Suggestions and contributions to peakPantheR are welcome, for more information please first refer to the contribution guide and code of conduct, or get in touch by opening a Github issue.

Copyright

peakPantheR is licensed under the GPLv3

As a summary, the GPLv3 license requires attribution, inclusion of copyright and license information, disclosure of source code and changes. Derivative work must be available under the same terms.

Owner

Name: National Phenome Centre
Login: phenomecentre
Kind: organization

Website: http://phenomecentre.org
Repositories: 4
Profile: https://github.com/phenomecentre

GitHub Events

Total

Member event: 1

Last Year

Member event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 409
Total Committers: 8
Avg Commits per committer: 51.125
Development Distribution Score (DDS): 0.259

Past Year

Commits: 19
Committers: 3
Avg Commits per committer: 6.333
Development Distribution Score (DDS): 0.211

Top Committers

Name	Email	Commits
Arnaud M. Wolfer	a**r@g**m	303
gscorreia89	g**9@g**m	39
adwolfer	a**2@i**k	32
Jake TM Pearce	j**t@g**m	12
Nitesh Turaga	n**a@g**m	12
Arnaud M. Wolfer	a**2@i**k	7
J Wokaty	j**y@s**u	2
J Wokaty	j****y	2

Committer Domains (Top 20 + Academic)

sph.cuny.edu: 1 ic.ac.uk: 1 imperial.ac.uk: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 5
Total pull requests: 36
Average time to close issues: 11 months
Average time to close pull requests: 3 days
Total issue authors: 4
Total pull request authors: 2
Average comments per issue: 2.8
Average comments per pull request: 1.03
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jaketmp (2)
JunYang2021 (1)
xulei99 (1)
pablovgd (1)

Pull Request Authors

adwolfer (31)
Gscorreia89 (5)

Top Labels

Issue Labels

enhancement (2)

Pull Request Labels

enhancement (14) bug (4)

Packages

Total packages: 1
Total downloads:
- bioconductor 9,705 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

bioconductor.org: peakPantheR

Peak Picking and Annotation of High Resolution Experiments

Homepage: https://github.com/phenomecentre/peakPantheR
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/peakPantheR/inst/doc/peakPantheR.pdf
License: GPL-3
Latest release: 1.22.0
published about 1 year ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 9,705 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Average: 24.5%

Downloads: 73.6%

Maintainers (1)

adwolfer@gmail.com

Last synced: 10 months ago

Dependencies

DESCRIPTION cran

R >= 4.2 depends
DT >= 0.15 imports
MSnbase >= 2.4.0 imports
XML >= 3.98.1.10 imports
bslib * imports
doParallel >= 1.0.11 imports
foreach >= 1.4.4 imports
ggplot2 >= 3.3.0 imports
gridExtra >= 2.3 imports
methods >= 3.4.0 imports
minpack.lm >= 1.2.1 imports
mzR >= 2.12.0 imports
pracma >= 2.2.3 imports
scales >= 0.5.0 imports
shiny >= 1.0.5 imports
shinycssloaders >= 1.0.0 imports
stringr >= 1.2.0 imports
utils * imports
BiocStyle * suggests
devtools * suggests
faahKO * suggests
knitr * suggests
msdata * suggests
pander * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/check-bioc-devel.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/check-bioc.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite