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pcaMethods

Perform PCA on data with missing values in R

https://github.com/hredestig/pcamethods

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
    2 of 31 committers (6.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.7%) to scientific vocabulary

Keywords

looking-for-maintainer

Keywords from Contributors

bioconductor-packages bioconductor bioinformatics mass-spectrometry metabolomics hdf5 rhdf5 genomics peak-detection feature-detection
Last synced: 11 months ago · JSON representation

Repository

Perform PCA on data with missing values in R

Basic Info
  • Host: GitHub
  • Owner: hredestig
  • License: gpl-2.0
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 1.78 MB
Statistics
  • Stars: 52
  • Watchers: 3
  • Forks: 11
  • Open Issues: 7
  • Releases: 0
Topics
looking-for-maintainer
Created over 10 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License

README.md

pcaMethods

R package for performing principal component analysis PCA with applications to missing value imputation. Provides a single interface to performing PCA using

  • SVD: a fast method which is also the standard method in R but which is not applicable for data with missing values.
  • NIPALS: an iterative fast method which is applicable also to data with missing values.
  • PPCA: Probabilistic PCA which is applicable also on data with missing values. Missing value estimation is typically better than NIPALS but also slower to compute and uses more memory. A port to R of the implementation by Jakob Verbeek.
  • BPCA: Bayesian PCA which performs very well in the presence of missing values but is slower than PPCA. A port of the matlab implementation by Shigeyuki Oba.
  • NLPCA: Non-linear PCA which can find curves in data and in presence of such can perform accurate missing value estimation. Matlab port of the implementation by Mathias Scholz.

pcaMethods is a Bioconductor package and you can install it by

R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("pcaMethods")

Documentation

R browseVignettes("pcaMethods") ?<function_name>

Owner

  • Name: Henning Redestig
  • Login: hredestig
  • Kind: user

GitHub Events

Total
  • Issues event: 1
  • Watch event: 6
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 6
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 353
  • Total Committers: 31
  • Avg Commits per committer: 11.387
  • Development Distribution Score (DDS): 0.836
Past Year
  • Commits: 32
  • Committers: 10
  • Avg Commits per committer: 3.2
  • Development Distribution Score (DDS): 0.656
Top Committers
Name Email Commits
Henning Redestig h****d@g****m 58
h.redestig h****g@b****8 53
stacklies@mpimp-golm.mpg.de s****s@m****e@b****8 29
unknown s****s@m****e 29
Dan Tenenbaum d****a@f****g 27
d.tenenbaum d****m@b****8 23
Henning Redestig h****d@g****m 22
Nitesh Turaga n****a@g****m 18
Herve Pages h****s@f****g 17
p.aboyoun p****n@b****8 13
Patrick Aboyoun u****n 13
hpages@fhcrc.org h****s@f****g@b****8 9
w.stacklies w****s@b****8 5
Wolfram Stacklies w****s@g****m 5
vobencha v****a@g****m 4
vobencha v****n@r****g 4
Hervé Pagès h****s@f****g 4
Kevin Wright k****t@g****m 2
J Wokaty j****y 2
Chao-Jen Wong c****2@f****g 2
J Wokaty j****y@s****u 2
LiNk-NY m****9@g****m 2
c.wong c****g@b****8 2
Martin Morgan m****n@f****g 1
Nishant Gopalakrishnan n****k@f****g 1
Seth Falcon s****n@f****g 1
Sonali Arora s****a@f****g 1
mtmorgan@fhcrc.org m****n@f****g@b****8 1
n.gopalakrishnan n****n@b****8 1
s.arora s****a@b****8 1
and 1 more...
Committer Domains (Top 20 + Academic)
fhcrc.org: 9 mpimp-golm.mpg.de: 2 sph.cuny.edu: 1 fredhutch.org: 1 roswellpark.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 21
  • Total pull requests: 4
  • Average time to close issues: 9 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 19
  • Total pull request authors: 3
  • Average comments per issue: 1.9
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • 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
  • iquasere (3)
  • StuntsPT (1)
  • sonali8434 (1)
  • hredestig (1)
  • topepo (1)
  • lxzdong (1)
  • petergaoshan (1)
  • bharris12 (1)
  • HedvigS (1)
  • Jfgrass (1)
  • flying-sheep (1)
  • fentouxungui (1)
  • stephanieherman (1)
  • runnytone (1)
  • CreaperLost (1)
Pull Request Authors
  • kwstat (2)
  • flying-sheep (1)
  • hredestig (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 707,853 total
  • Total dependent packages: 19
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: pcaMethods

A collection of PCA methods

  • Versions: 5
  • Dependent Packages: 19
  • Dependent Repositories: 0
  • Downloads: 707,853 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 3.2%
Average: 3.5%
Downloads: 3.7%
Stargazers count: 4.6%
Forks count: 6.3%
Maintainers (1)
henning.red@gmail.com
Last synced: 11 months ago