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Rdisop

This is the git repository matching the Bioconductor package Rdisop: Decomposition of Isotopic Patterns

https://github.com/sneumann/rdisop

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    2 of 18 committers (11.1%) from academic institutions
  • ○
    Institutional organization owner
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    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

mass-spectrometry metabolomics r

Keywords from Contributors

bioconductor-package genomics bioconductor bioinformatics feature-detection peak-detection proteomics looking-for-maintainer gene single-cell-rna-seq
Last synced: 7 months ago · JSON representation

Repository

This is the git repository matching the Bioconductor package Rdisop: Decomposition of Isotopic Patterns

Basic Info
Statistics
  • Stars: 4
  • Watchers: 7
  • Forks: 9
  • Open Issues: 0
  • Releases: 0
Topics
mass-spectrometry metabolomics r
Created about 12 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
library(Rdisop)
```

# Rdisop


[![R-CMD-check](https://github.com/janlisec/Rdisop/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/janlisec/Rdisop/actions/workflows/R-CMD-check.yaml)
[![DOI](https://img.shields.io/badge/doi-10.1093/bioinformatics/btm631-yellow.svg)](https://doi.org/10.1093/bioinformatics/btm631)


In high resolution mass spectrometry (HR-MS), the measured masses can be 
decomposed into potential element combinations (chemical sum formulas). 
Where additional mass/intensity information of respective isotopic peaks is
available, decomposition can take this information into account to better
rank the potential candidate sum formulas. To compare measured mass/intensity
information with the theoretical distribution of candidate sum formulas, the
latter needs to be calculated.
This package implements fast algorithms to address both tasks, the 
calculation of isotopic distributions for arbitrary sum formulas (assuming a
HR-MS resolution of roughly 30,000), and the ranked list of sum formulas
fitting an observed peak or isotopic peak set.

## Installation

You can install the development version of **Rdisop** using:

``` r
# install.packages("devtools")
devtools::install_github("sneumann/Rdisop")
```

## Example

The user can use built in sets of chemical elements or define such sets 
specifically and get informations on a specified sum formula, *i.e.* the
isotopic distribution which would be observed in HR-MS.

```{r exmpl2}
ele <- initializeElements(c("C","H","N","O","Mg"))
chlorophyll <- getMolecule("C55H72MgN4O5H", elements = ele)
getIsotope(chlorophyll, 1:4)
```

For individual masses, potential molecules can be calculated.

```{r exmpl3}
decomposeMass(mass = 46.042, ppm = 20, maxisotopes = 4)
```

This decomposition can also be performed for measurements containing several 
isotopes.

```{r exmpl5}
# glutamic acid (C5H9NO4)
mol <- decomposeIsotopes(masses = c(147.053, 148.056), intensities = c(93, 5.8))
data.frame(getFormula(mol), getScore(mol), getValid(mol))
```

Owner

  • Name: Steffen Neumann
  • Login: sneumann
  • Kind: user

GitHub Events

Total
  • Issues event: 10
  • Issue comment event: 61
  • Push event: 20
  • Pull request review comment event: 12
  • Pull request review event: 10
  • Pull request event: 19
  • Create event: 3
Last Year
  • Issues event: 10
  • Issue comment event: 61
  • Push event: 20
  • Pull request review comment event: 12
  • Pull request review event: 10
  • Pull request event: 19
  • Create event: 3

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 234
  • Total Committers: 18
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.496
Past Year
  • Commits: 19
  • Committers: 5
  • Avg Commits per committer: 3.8
  • Development Distribution Score (DDS): 0.684
Top Committers
Name Email Commits
s.neumann s****n@b****8 118
d.tenenbaum d****m@b****8 27
Steffen Neumann s****n@i****e 18
Nitesh Turaga n****a@g****m 14
p.aboyoun p****n@b****8 12
J Wokaty j****y 8
hpages@fhcrc.org h****s@f****g@b****8 8
J Wokaty j****y@s****u 6
David Rasp d****p@g****m 5
yufree y****e@l****n 5
Hervé Pagès h****s@f****g 2
mjhelf m****8@c****u 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
rickhelmus 3****s 2
Kayla-Morrell k****l@r****g 1
Mike Smith g****h@g****m 1
c.wong c****g@b****8 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 cornell.edu: 1 fredhutch.org: 1 live.cn: 1 sph.cuny.edu: 1 fhcrc.org: 1 ipb-halle.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 23
  • Total pull requests: 24
  • Average time to close issues: over 4 years
  • Average time to close pull requests: 11 days
  • Total issue authors: 12
  • Total pull request authors: 7
  • Average comments per issue: 5.22
  • Average comments per pull request: 1.0
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 18
  • Average time to close issues: 8 months
  • Average time to close pull requests: 15 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 3.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sneumann (10)
  • stanstrup (2)
  • cbielow (2)
  • cbroeckl (1)
  • Rennepink (1)
  • janlisec (1)
  • sonali-bioc (1)
  • agnesblch (1)
  • wkumler (1)
  • yufree (1)
  • jorainer (1)
  • ricoderks (1)
  • mhische-md (1)
Pull Request Authors
  • janlisec (17)
  • sneumann (7)
  • rickhelmus (2)
  • Livia-Rasp (2)
  • grimbough (1)
  • mjhelf (1)
  • yufree (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 124,174 total
  • Total dependent packages: 2
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: Rdisop

Decomposition of Isotopic Patterns

  • Versions: 5
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 124,174 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 4.1%
Downloads: 12.3%
Maintainers (1)
sneumann@ipb-halle.de
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.0.0 depends
  • Rcpp * depends
  • RUnit * suggests