anwarbio / bioassays

Bioassays

'Bioassays' is an R package, designed to provide a wide range of functions relevant to multi-well plate assays. It can handle data from any of the standard multi-well plate format: 6, 12, 24, 96 or 384 well plates. ‘Bioassays’ can help in formatting, visualizing and analyzing multi-well plate data. It has functions for handling outliers, for handling multiple data sets with separate blanks, for estimating values from standard curves, for summarizing data and for doing statistical analysis. Moreover, it is strongly documented in a manner designed to be easy for even beginners to grasp.

Installation

You can install the released version of bioassays from CRAN with:

install.packages("bioassays")

The latest development version can be installed from github with the remotes package

library(remotes)
install_github("anwarbio/bioassays")

Example

Detail’s of various funtions in this package is provided in ‘bioassays-vignette’. Examples on how to use this package is provided in ‘bioassays-example’ in Vignette.

License: GPL-3.0

https://github.com/anwarbio/bioassays/blob/master/LICENSE

Contribute

We love your input! Users may request new features by opening a GitHub Issue, or may contribute their own additions and improvements via a pull request. Similarly, if you run into problems while using this package, or require technical support, do not hesitate to request support through a GitHub Issue. If you use ‘Bioassays’ in your work and would like to further collaborate, I would be more than willing to discuss it over email or GitHub Issue. When you submit code changes, your submissions are understood to be under the same GPL-3.0 that covers this project.

An incomplete list of possible improvements:

• Include support for qPCR data analysis
• Include provisions for user template
• Include capability for plotting data

bioassays's Issues

[JOSS REVIEW] Contribution guidelines

Please add some simple Community guidelines: for third parties wishing to

1. Contribute to the software
2. Report issues or problems with the software
3. Seek support

You can add these instructions in a CONTRIBUTIONS.md file.

For inspiration, here is a an example from the workflowr package.

plate2df function not working properly

I imported data with readxl and converted it to plate format using data2plateformat. I got a variable with all the numbers (when checking with typeof() it is a list, when checking with class() it is "tbl_df" "tbl" "data.frame") and then wanted to convert that to a data frame using plate2df, but I got a dataframe with no values (where the number is supposed to be, it is a NA). Row, col, and position are filled in correctly.

I attached the corresponding data file and the code and the result is below:

OD_raw <- read_excel("96well_plate.xlsx")
OD_plate <- data2plateformat(OD_raw, platetype = 96)
OD_df <- plate2df(OD_plate); head(OD_df)

head(OD_df)
  row col position value
1   A   1      A01    NA
2   A   2      A02    NA
3   A   3      A03    NA
4   A   4      A04    NA
5   A   5      A05    NA
6   A   6      A06    NA

Thanks for your help.

Best, Ana

96well_plate.xlsx

[JOSS REVIEW]: R CMD check warning and note

Hi @anwarbio,

thank you for submitting your manuscript to JOSS. Great work!
I am one of the two assigned reviewers and will file issues for any suggestions I have here. Please feel free to respond with question or comments if anything is unclear or you disagree!

When I ran R CMD check on the package's source code, there was one warning because two of the included filenames contain spaces:

Found the following files with non-portable file names:
    inst/exdata/L HEPG2 P3 72HRS.csv
    inst/exdata/metafile 384 plate.csv
  These are not fully portable file names.
  See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

It would be great to replace the spaces with underscores (also to keep CRAN happy).

There was also the following Note:

File
    LICENSE
  is not mentioned in the DESCRIPTION file.
  Non-standard files/directories found at top level:
    ‘data-raw’ ‘figure1.png’ ‘figure2.png’ ‘figure3.png’ ‘figure4.png’
    ‘paper.bib’ ‘paper.md’

1. The DESCRIPTION currently refers to GPL 3 as the license. I think CRAN uses GPL-3 as the official abbreviation, see here.
   Right now, it seems that CRAN ignores the 3 suffix in your license declaration and expands it to GPL-2 and GPL-3. Hence, I believe the best line for your DESCRIPTION file would be

License: GPL-3 + file LICENSE

2. The Note also says Non-standard files/directories found at top level. These files are your actual manuscript. Adding them to the .buildignorefile will silence this part of theNote, e.g. your .buildignore` file could look like this:

^.*\.Rproj$
^\.Rproj\.user$
data-raw
figure1.png
figure2.png
figure3.png
figure4.png
paper.bib
paper.md

These two changes to the DESCRIPTION file silence the note.

[JOSS REVIEW]: installation instructions from github

Thanks a lot for including installation instructions for both CRAN and github. I believe the use of the install_github command requires that the remotes package is attached first. How about this:

The latest development version can be installed from github with the remotes package:

library(remotes)
install_github("anwarbio/bioassays")