Data

Tools

Indexes

Applications

Experiments

Open Source Science

condiments

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

https://github.com/hectorrdb/condiments

Science Score: 46.0%

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
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

Basic Info
Statistics
  • Stars: 29
  • Watchers: 3
  • Forks: 5
  • Open Issues: 7
  • Releases: 2
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

R-CMD-check Codecov test coverage Generic badge DOI

R package: condiments

Installation

You can install the condiments from bioconductor using

r if(!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("condiments")

To install the development version in R, run:

r if(!requireNamespace("devtools", quietly = TRUE)) { install.packages("devtools") } devtools::install_github("HectorRDB/condiments")

The installation should only take a few seconds. The dependencies of the package are listed in the DESCRIPTION file of the package.

Issues and bug reports

Please use https://github.com/HectorRDB/condiments/issues to submit issues, bug reports, and comments.

Usage

Start with the vignette online or explore on of our case studies in the paper here.

Owner

  • Name: Hector Roux de Bézieux
  • Login: HectorRDB
  • Kind: user

PhD Student in Biostatistics at UC Berkeley

GitHub Events

Total
  • Issues event: 7
  • Watch event: 5
  • Delete event: 1
  • Issue comment event: 10
  • Push event: 8
  • Pull request event: 1
  • Fork event: 2
  • Create event: 1
Last Year
  • Issues event: 7
  • Watch event: 5
  • Delete event: 1
  • Issue comment event: 10
  • Push event: 8
  • Pull request event: 1
  • Fork event: 2
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 176
  • Total Committers: 2
  • Avg Commits per committer: 88.0
  • Development Distribution Score (DDS): 0.034
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Hector h****x@b****u 170
Nitesh Turaga n****a@g****m 6
Committer Domains (Top 20 + Academic)
berkeley.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 7
  • Total pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 7
  • Total pull request authors: 0
  • Average comments per issue: 1.57
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Alexis-Varin (2)
  • jiw181 (1)
  • khsjh (1)
  • MartaSanchezCarbonell (1)
  • GilbertHan1011 (1)
  • anemartinezlarrinaga2898 (1)
  • Jaimelan (1)
  • chungsai (1)
  • AndreaYCT (1)
  • JesseRop (1)
  • Yanst86 (1)
  • cgoneill (1)
  • klai001 (1)
  • AAlhendi1707 (1)
Pull Request Authors
  • HectorRDB (1)
  • AndreaYCT (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 9,460 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: condiments

Differential Topology, Progression and Differentiation

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 9,460 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 27.1%
Downloads: 81.2%
Maintainers (1)
hector.rouxdebezieux@berkeley.edu
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • BiocParallel * imports
  • Ecume >= 0.9.1 imports
  • RANN * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • TrajectoryUtils * imports
  • distinct * imports
  • dplyr >= 1.0 imports
  • igraph * imports
  • magrittr * imports
  • matrixStats * imports
  • methods * imports
  • mgcv * imports
  • pbapply * imports
  • slingshot >= 1.9 imports
  • stats * imports
  • utils * imports
  • RColorBrewer * suggests
  • TSCAN * suggests
  • covr * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • randomForest * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tidyr * suggests
  • viridis * suggests
.github/workflows/Devel.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite