detrendr

An R package for detrending images.

https://github.com/rorynolan/detrendr

Science Score: 39.0%

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
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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Found 2 DOI reference(s) in README
○
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Committers with academic emails
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (18.2%) to scientific vocabulary

Last synced: 9 months ago · JSON representation

Repository

An R package for detrending images.

Basic Info

Host: GitHub
Owner: rorynolan
License: other
Language: R
Default Branch: master
Homepage: https://rorynolan.github.io/detrendr/
Size: 30.1 MB

Statistics

Stars: 3
Watchers: 1
Forks: 1
Open Issues: 0
Releases: 6

Created over 8 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License Codemeta

README.Rmd

---
output: github_document
---

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

# `detrendr`  

Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy (FCS and FFS) analysis. This package contains functionality published in a 2016 paper https://doi.org/10.1093/bioinformatics/btx434 but it has been extended since then with the _Robin Hood_ algorithm and thus contains unpublished work.

[![R-CMD-check](https://github.com/rorynolan/detrendr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rorynolan/detrendr/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/github/rorynolan/detrendr/graph/badge.svg?token=GkXMOLXlAH)](https://codecov.io/github/rorynolan/detrendr)

[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/detrendr)](https://cran.r-project.org/package=detrendr)
![RStudio CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/detrendr)
![RStudio CRAN monthly downloads](https://cranlogs.r-pkg.org/badges/detrendr)

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)


## Installation

You can install the release version of `detrendr` from [CRAN](https://CRAN.R-project.org/package=detrendr) with:

```{r, eval=FALSE}
install.packages("detrendr")
```

You can install the (unstable) development version of `detrendr` from [GitHub](https://github.com/rorynolan/detrendr/) with:

```{r, eval=FALSE}
devtools::install_github("rorynolan/detrendr")
```

I highly recommend using the release version. The dev version is just for the ultra-curious and should be thought of as unreliable.


## How to use the package

See the package website at https://rorynolan.github.io/detrendr/.


## Contribution
Contributions to this package are welcome. The preferred method of contribution is through a github pull request. Feel free to contact me by creating an issue. Please note that this project is released with a [Contributor Code of Conduct](https://github.com/rorynolan/detrendr/blob/master/CONDUCT.md). By participating in this project you agree to abide by its terms.

Owner

Name: Rory Nolan
Login: rorynolan
Kind: user
Location: Oakland, California.

Website: http://rorynolan.rbind.io
Repositories: 7
Profile: https://github.com/rorynolan

Data scientist at mirvie.com. PhD in statistical image analysis.

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  ],
  "developmentStatus": [
    "https://www.repostatus.org/#active",
    "https://lifecycle.r-lib.org/articles/stages.html"
  ]
}

GitHub Events

Total

Push event: 28

Last Year

Push event: 28

Committers

Last synced: over 2 years ago

All Time

Total Commits: 160
Total Committers: 2
Avg Commits per committer: 80.0
Development Distribution Score (DDS): 0.006

Past Year

Commits: 8
Committers: 1
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Rory Nolan	r**n@g**m	159
Lionel Henry	l**y@g**m	1

Issues and Pull Requests

Last synced: over 1 year ago

All Time

Total issues: 6
Total pull requests: 2
Average time to close issues: 7 months
Average time to close pull requests: 23 days
Total issue authors: 4
Total pull request authors: 2
Average comments per issue: 2.83
Average comments per pull request: 0.5
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rorynolan (3)
cb12ag (1)
Cumol (1)
kevinushey (1)

Pull Request Authors

andrjohns (2)
lionel- (1)

Top Labels

Issue Labels

enhancement (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 1,019 last-month

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 20
Total maintainers: 1

cran.r-project.org: detrendr

Detrend Images

Homepage: https://rorynolan.github.io/detrendr/
Documentation: http://cran.r-project.org/web/packages/detrendr/detrendr.pdf
License: BSD_3_clause + file LICENSE
Latest release: 0.6.15
published about 3 years ago

Versions: 20
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 1,019 Last month

Rankings

Downloads: 17.1%

Dependent packages count: 18.1%

Forks count: 21.0%

Average: 21.2%

Dependent repos count: 24.0%

Stargazers count: 25.5%

Maintainers (1)

rorynoolan@gmail.com

Last synced: 10 months ago

Dependencies

DESCRIPTION cran

R >= 3.1 depends
Rcpp >= 1.0.1 imports
RcppParallel >= 5.0.2 imports
arrayhelpers >= 1.1.0 imports
autothresholdr >= 1.3.11 imports
checkmate >= 1.9.3 imports
doParallel * imports
dplyr * imports
filesstrings >= 3.2 imports
foreach * imports
ijtiff >= 2.2 imports
iterators * imports
magrittr >= 1.5 imports
parallel * imports
plyr * imports
purrr * imports
rlang >= 0.3.3 imports
stringr >= 1.4 imports
tools * imports
withr >= 2.1 imports
MASS * suggests
R.utils * suggests
abind * suggests
covr * suggests
ggplot2 * suggests
glue >= 1.3.0 suggests
graphics * suggests
gridExtra * suggests
knitr * suggests
lattice * suggests
matrixStats * suggests
mgcv * suggests
pacman * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 3.0 suggests
tidyr * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

detrendr

Science Score: 39.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: detrendr

Rankings

Maintainers (1)

Dependencies