Number and Brightness Image Analysis

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 .


News

nandb 2.0.0

MAJOR CHANGES

  • Robin Hood detrending is now used instead of exponential smoothing detrending. This is a breaking change.

NEW FEATURES

  • The timeseries functions now have the option to overlap for better time resolution.
  • A pkgdown website!

nandb 1.1.0

NEW FEATURES

  • matrix_raster_plot() is back. I thought it didn't really fit but a user said they missed when it was gone so it's back now.

nandb 1.0.1

BUG FIXES

  • Fix issues on CRAN linux devel clang.

nandb 1.0.0

NEW FEATURES

  • The package is now peer-reviewed and published in the journal Bioinformatics. See citation("nandb").
  • The package style is now in accordance with the tidyverse style guide.
  • brightness() and number() now include options to set offset, S-factor, readout_noise and gamma correction terms.
  • brightness() and number() now enable calculation of both definitions ("B" and "epsilon"; "N" and "n") of brightness and number.
  • Detrending is outsourced to the detrendr package. This new package makes detrending more accurate and much faster.
  • TIFF I/O and graphics display() are now outsourced to the ijtiff package. This means R users no longer have to tell nandb how many channels are in the images.
  • The package now has its own S3 class system.

BUG FIXES

  • Kmer calculations are no longer possible. The way in which they were done was over-simple.

nandb 0.2.1

BUG FIXES

  • Compatible with filesstrings 1.1.0.

nandb 0.2.0

  • The first version that I consider CRAN-worthy.

Reference manual

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install.packages("nandb")

2.0.2 by Rory Nolan, 10 days ago


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


Report a bug at https://github.com/rorynolan/nandb/issues


Browse source code at https://github.com/cran/nandb


Authors: Rory Nolan [aut, cre, cph] , Luis Alvarez [ctb, cph] , Sergi Padilla-Parra [ctb, ths, cph]


Documentation:   PDF Manual  


BSD_3_clause + file LICENSE license


Imports Rcpp, filesstrings, magrittr, autothresholdr, dplyr, stringr, purrr, checkmate, detrendr, ijtiff, rlang, reshape2, viridis, glue, BBmisc, ggplot2, assertthat, withr, utils

Suggests knitr, rmarkdown, covr, testthat, abind, tidyr, gridExtra, pacman, matrixStats, spelling

Linking to Rcpp


See at CRAN