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`nandb`

Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper. The seminal paper for the technique is Digman et al. 2008. A review of the technique was published in 2017.

Installation

You can install the release version of nandb from CRAN with:

install.packages("nandb")

You can install the (unstable) development version of nandb from GitHub with:

devtools::install_github("rorynolan/nandb")

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/nandb/.

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. By participating in this project you agree to abide by its terms.

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Version

Install

install.packages('nandb')

Monthly Downloads

418

Version

2.1.0

License

BSD_3_clause + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/rorynolan/nandb

Homepage

https://rorynolan.github.io/nandb/

Maintainer

Rory Nolan

Last Published

May 16th, 2021

Functions in nandb (2.1.0)

Calculate brightness from image series.

cc_brightness_timeseries_folder

Cross-correlated brightness time-series calculations for every image in a folder.

cc-nb-ts-img-classes

Cross-correlated number and brightness time series image classes.

Cross-correlated brightness.

cc-nb-img-classes

Cross-correlated number and brightness image classes.

brightness_folder

Brightness calculations for every image in a folder.

cc_brightness_folder

Cross-correlated brightness calculations for every image in a folder.

brightness_timeseries

Create a brightness time-series.

cc_brightness_timeseries

Create a cross-correlated brightness time-series.

brightness_timeseries_folder

Brightness time-series calculations for every image in a folder.

nandb: Number and brightness in R.

Calculate number from image series.

cc_number_timeseries_folder

Cross-correlated number time-series calculations for every image in a folder.

Number and brightness image classes.

nb-ts-img-classes

Number and brightness time series image classes.

cc_number_timeseries

Create a cross-correlated number time-series.

matrix_raster_plot

Make a raster plot of a matrix.

Smooth and median filters with options for handling NAs.

Calculate the cross-variance of two vectors.

cross_var_pillars

Calculate the cross-variance of corresponding pillars of 3d arrays.

Cross-correlated number.

cc_number_folder

Cross-correlated number calculations for every image in a folder.

Number calculations for every image in a folder.

number_timeseries

Create a number time-series.

number_timeseries_folder

Number time-series calculations for every image in a folder.