Data

Tools

Indexes

Applications

Experiments

Open Source Science

IPO

A Tool for automated Optimization of XCMS Parameters

https://github.com/rietho/ipo

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 20 committers (5.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioinformatics mass-spectrometry bioconductor peak-detection feature-detection core-package gene metabolomics genomics
Last synced: 11 months ago · JSON representation

Repository

A Tool for automated Optimization of XCMS Parameters

Basic Info
Statistics
  • Stars: 34
  • Watchers: 8
  • Forks: 20
  • Open Issues: 17
  • Releases: 0
Created over 11 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

IPO

How long since the package was first in a released Bioconductor version (or is it in devel only). Percentile (top 5/20/50% or 'available') of downloads over last 6 full months. Comparison is done across all package categories (software, annotation, experiment). Project Status: Unsupported – The project has reached a stable, usable state but the author(s) have ceased all work on it. A new maintainer may be desired.

Latest release: Build Status Biocondcutor Release Devel: Build Status Biocondcutor Devel codecov @master: Build Status Travis-CI

IPO (‘Isotopologue Parameter Optimization’) is a tool for automated Optimization of XCMS Parameters. It is a fast and free of labeling steps, and applicable to data from different kinds of samples and data from different methods of liquid chromatography - high resolution mass spectrometry and data from different instruments.

Find out more about the usage in the package vignette (Biocondcutor development version). The publication is available from http://www.biomedcentral.com/1471-2105/16/118.

Installation

Get the latest release version from Bioconductor: ```{r}

try http:// if https:// URLs are not supported

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("IPO") ````

Or the development version from Github:

```R

install.packages("devtools")

devtools::install_github("rietho/IPO") ```

Owner

  • Name: Thomas Lieb
  • Login: rietho
  • Kind: user

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 245
  • Total Committers: 20
  • Avg Commits per committer: 12.25
  • Development Distribution Score (DDS): 0.596
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Thomas Riebenbauer t****r@j****t 99
Gunnar Libiseller g****r@j****t 34
Thomas Riebenbaur T****r@j****t 27
t.riebenbauer t****r@b****8 25
Nitesh Turaga n****a@g****m 14
Steffen Neumann s****n@i****e 13
Pablo Moreno p****o@g****m 5
Herve Pages h****s@f****g 4
hpages@fhcrc.org h****s@f****g@b****8 4
Hervé Pagès h****s@f****g 3
J Wokaty j****y@s****u 2
Martin Morgan m****n@f****g 2
Steffen Neumann s****e 2
lshep l****d@r****g 2
mtmorgan@fhcrc.org m****n@f****g@b****8 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Thomas Lieb 1****o 1
Kayla-Morrell k****l@r****g 1
LiNk-NY m****9@g****m 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 4 roswellpark.org: 3 joanneum.at: 3 sph.cuny.edu: 1 fredhutch.org: 1 ipb-halle.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 72
  • Total pull requests: 4
  • Average time to close issues: 5 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 36
  • Total pull request authors: 3
  • Average comments per issue: 3.22
  • Average comments per pull request: 3.5
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sneumann (16)
  • tobigithub (13)
  • rietho (3)
  • etrh (3)
  • ghost (2)
  • lauzikaite (2)
  • Jiaqc (2)
  • Titan100 (2)
  • mheiser-md (2)
  • leichtle (1)
  • lecorguille (1)
  • danagibbon (1)
  • tew42 (1)
  • jorainer (1)
  • jjkellogg (1)
Pull Request Authors
  • sneumann (2)
  • pcm32 (1)
  • tobigithub (1)
Top Labels
Issue Labels
enhancement (6) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 24,875 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: IPO

Automated Optimization of XCMS Data Processing parameters

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 24,875 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 2.4%
Stargazers count: 4.7%
Average: 9.4%
Downloads: 40.0%
Maintainers (1)
thomas.r.lieb@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • CAMERA * depends
  • grDevices * depends
  • graphics * depends
  • rsm * depends
  • stats * depends
  • utils * depends
  • xcms >= 1.50.0 depends
  • parallel * enhances
  • BiocParallel * imports
  • BiocGenerics * suggests
  • RUnit * suggests
  • faahKO * suggests
  • knitr * suggests
  • msdata * suggests
  • mtbls2 * suggests