tread

tread is an R package to extract data from Excel files generated by Tecan Infinite 200 Pro plate readers

https://github.com/gl-eb/tread

Science Score: 67.0%

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

✓
CITATION.cff file
Found 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
Links to: zenodo.org
○
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Low similarity (15.4%) to scientific vocabulary

Keywords

bioinformatics r tecan

Last synced: 6 months ago · JSON representation ·

Repository

tread is an R package to extract data from Excel files generated by Tecan Infinite 200 Pro plate readers

Basic Info

Host: GitHub
Owner: gl-eb
License: other
Language: R
Default Branch: main
Homepage: https://www.gl-eb.me/tread/
Size: 6.15 MB

Statistics

Stars: 1
Watchers: 1
Forks: 0
Open Issues: 1
Releases: 9

Topics

bioinformatics r tecan

Created almost 4 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
---



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

# tread 


[![R-CMD-check](https://github.com/gl-eb/tread/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/gl-eb/tread/actions/workflows/R-CMD-check.yaml)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10200272.svg)](https://doi.org/10.5281/zenodo.10200272)


tread is an R package to extract data from Excel files generated by Tecan Infinite 200 Pro plate readers.

## Installation

You can install tread from [GitHub](https://github.com/gl-eb/tread) with:

``` r
# install.packages("devtools")
devtools::install_github("gl-eb/tread")
```

To install the package including the vignette:

```r
devtools::install_github("gl-eb/tread", dependencies = TRUE, build_vignettes = TRUE)
```

### Development Version

You can also install the development version.
While it may contain unreleased features, changes or bugfixes, it is also likely to rapidly evolve, potentially breaking your code.
Do not use the development version if you are not willing to deal with this.

``` r
devtools::install_github("gl-eb/tread", ref = "develop")
```

## Hot To Use

Examples of analysis workflows are documented in `vignette("tread")`

```{r loading}
library(tread)
```

```{r example-custom, eval = FALSE}
# parse your own set of measurements
dat <- tparse("path/to/file.xlsx")

# specify sheet of the excel file (default: 1)
dat <- tparse("path/to/file.xlsx", sheet = 3)

# unite multiple segments of a time series of measurements
dat <- tunite("path/to/file.xlsx")

# specify with which sheets to start and how many to include
dat <- tunite("path/to/file.xlsx", segments = 2, start = 1)
```

## Acknowledgements

Tecan® is a trademark of Tecan Group Ltd., Männedorf, Switzerland.
The authors have no affiliation with them other than being users of their products.

The plate reader icon was designed by [kehan](https://github.com/kehantan) and is licensed under [CC0](https://creativecommons.org/publicdomain/zero/1.0/)

Owner

Name: Gleb Ebert
Login: gl-eb
Kind: user
Company: ETH Zurich

Website: glebsite.ch
Twitter: gl_eb
Repositories: 4
Profile: https://github.com/gl-eb

PhD student in evolutionary microbiology

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "tread" in publications use:'
type: software
license: MIT
title: 'tread: Read Tecan Infinite 200 Pro Data'
version: 0.5.2.9000
doi: 10.5281/zenodo.10200272
abstract: Read Excel files generated by a Tecan Infinite 200 Pro plate reader. The
  data is returned in tidy format ready for downstream analysis or plotting.
authors:
- family-names: Ebert
  given-names: Gleb G.
  email: dev@gl-eb.me
  orcid: https://orcid.org/0000-0002-7734-3824
preferred-citation:
  type: manual
  title: 'tread: Read Tecan Infinite 200 Pro Data'
  authors:
  - family-names: Ebert
    given-names: Gleb
  year: '2023'
  publisher:
    name: Zenodo
  notes: R package, https://github.com/gl-eb/tread/
  doi: 10.5281/zenodo.10200272
  url: https://www.gl-eb.me/tread/
repository-code: https://github.com/gl-eb/tread
url: https://www.gl-eb.me/tread/
contact:
- family-names: Ebert
  given-names: Gleb G.
  email: dev@gl-eb.me
  orcid: https://orcid.org/0000-0002-7734-3824
keywords:
- bioinformatics
- r
- tecan
references:
- type: software
  title: cli
  abstract: 'cli: Helpers for Developing Command Line Interfaces'
  notes: Imports
  url: https://cli.r-lib.org
  repository: https://CRAN.R-project.org/package=cli
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2024'
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  url: https://r-datatable.com
  repository: https://CRAN.R-project.org/package=data.table
  authors:
  - family-names: Barrett
    given-names: Tyson
    email: t.barrett88@gmail.com
  - family-names: Dowle
    given-names: Matt
    email: mattjdowle@gmail.com
  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  - family-names: Gorecki
    given-names: Jan
  - family-names: Chirico
    given-names: Michael
  - family-names: Hocking
    given-names: Toby
    orcid: https://orcid.org/0000-0002-3146-0865
  year: '2024'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2024'
- type: software
  title: fs
  abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
  notes: Imports
  url: https://fs.r-lib.org
  repository: https://CRAN.R-project.org/package=fs
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Wickham
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    email: hadley@posit.co
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2024'
- type: software
  title: janitor
  abstract: 'janitor: Simple Tools for Examining and Cleaning Dirty Data'
  notes: Imports
  url: https://sfirke.github.io/janitor/
  repository: https://CRAN.R-project.org/package=janitor
  authors:
  - family-names: Firke
    given-names: Sam
    email: samuel.firke@gmail.com
  year: '2024'
- type: software
  title: lifecycle
  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
  notes: Imports
  url: https://lifecycle.r-lib.org/
  repository: https://CRAN.R-project.org/package=lifecycle
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  year: '2024'
- type: software
  title: lubridate
  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
  notes: Imports
  url: https://lubridate.tidyverse.org
  repository: https://CRAN.R-project.org/package=lubridate
  authors:
  - family-names: Spinu
    given-names: Vitalie
    email: spinuvit@gmail.com
  - family-names: Grolemund
    given-names: Garrett
  - family-names: Wickham
    given-names: Hadley
  year: '2024'
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  year: '2024'
- type: software
  title: readxl
  abstract: 'readxl: Read Excel Files'
  notes: Imports
  url: https://readxl.tidyverse.org
  repository: https://CRAN.R-project.org/package=readxl
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2024'
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  version: '>= 1.1.0'
  year: '2024'
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  url: https://stringr.tidyverse.org
  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2024'
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  abstract: 'tidyselect: Select from a Set of Strings'
  notes: Imports
  url: https://tidyselect.r-lib.org
  repository: https://CRAN.R-project.org/package=tidyselect
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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  notes: Imports
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
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    given-names: Hadley
    email: hadley@posit.co
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    given-names: Winston
  year: '2024'
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  notes: Suggests
  url: https://docs.ropensci.org/cffr/
  repository: https://CRAN.R-project.org/package=cffr
  authors:
  - family-names: Hernangómez
    given-names: Diego
    email: diego.hernangomezherrero@gmail.com
    orcid: https://orcid.org/0000-0001-8457-4658
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  url: https://github.com/eclarke/ggbeeswarm
  repository: https://CRAN.R-project.org/package=ggbeeswarm
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    given-names: Erik
    email: erikclarke@gmail.com
  - family-names: Sherrill-Mix
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  url: https://jpquast.github.io/ggplate/
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  authors:
  - family-names: Quast
    given-names: Jan-Philipp
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    orcid: https://orcid.org/0000-0003-2713-778X
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  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
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    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
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    orcid: https://orcid.org/0000-0002-1576-2126
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    given-names: Lionel
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    orcid: https://orcid.org/0000-0002-9415-4582
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    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
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  url: https://yihui.org/knitr/
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    given-names: Yihui
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    orcid: https://orcid.org/0000-0003-0645-5666
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  repository: https://CRAN.R-project.org/package=rmarkdown
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    email: jj@posit.co
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    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
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    given-names: Christophe
    email: cderv@posit.co
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    email: kevin@posit.co
  - family-names: Atkins
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    given-names: Hadley
    email: hadley@posit.co
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    email: joe@posit.co
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    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
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    orcid: https://orcid.org/0000-0003-3925-190X
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    email: hadley@posit.co
  year: '2024'
  version: '>= 3.0.0'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 4.1.0'

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Dependencies

DESCRIPTION cran

R >= 2.10 depends
data.table * imports
dplyr * imports
janitor * imports
magrittr * imports
purrr * imports
readxl * imports
stringr * imports
tibble * imports
utils * imports
testthat >= 3.0.0 suggests

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

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JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v4 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/test-coverage.yaml actions

actions/checkout v4 composite
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