nandb v2.0.7
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Number and Brightness Image Analysis
Calculation of molecular number and brightness from
fluorescence microscopy image series. The software was published in a
2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for
the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>.
A review of the technique was published in 2017
<doi:10.1016/j.ymeth.2017.12.001>.
Readme
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.
Functions in nandb
| Name | Description | |
| cc_brightness_folder | Cross-correlated brightness calculations for every image in a folder. | |
| number_timeseries | Create a number time-series. | |
| number_folder | Number calculations for every image in a folder. | |
| cross_var_pillars | Calculate the cross-variance of corresponding pillars of 3d arrays. | |
| cross_var | Calculate the cross-variance of two vectors. | |
| cc_number_timeseries_folder | Cross-correlated number time-series calculations for every image in a folder. | |
| matrix_raster_plot | Make a raster plot of a matrix. | |
| number | Calculate number from image series. | |
| cc_number_timeseries | Create a cross-correlated number time-series. | |
| nb-ts-img-classes | Number and brightness time series image classes. | |
| cc_number | Cross-correlated number. | |
| median_filter | Smooth and median filters with options for handling NAs. | |
| cc_number_folder | Cross-correlated number calculations for every image in a folder. | |
| nandb | nandb: Number and brightness in R. | |
| nb-img-classes | Number and brightness image classes. | |
| number_timeseries_folder | Number time-series calculations for every image in a folder. | |
| cc-nb-ts-img-classes | Cross-correlated number and brightness time series image classes. | |
| brightness | Calculate brightness from image series. | |
| brightness_folder | Brightness calculations for every image in a folder. | |
| cc_brightness_timeseries_folder | Cross-correlated brightness time-series calculations for every image in a folder. | |
| cc-nb-img-classes | Cross-correlated number and brightness image classes. | |
| cc_brightness_timeseries | Create a cross-correlated brightness time-series. | |
| cc_brightness | Cross-correlated brightness. | |
| brightness_timeseries | Create a brightness time-series. | |
| brightness_timeseries_folder | Brightness time-series calculations for every image in a folder. | |
| No Results! | ||
Vignettes of nandb
| Name | ||
| batch-mode.Rmd | ||
| brightness-timeseries.Rmd | ||
| single-images.Rmd | ||
| No Results! | ||
Last month downloads
Details
| Type | Package |
| License | BSD_3_clause + file LICENSE |
| URL | https://rorynolan.github.io/nandb, https://github.com/rorynolan/nandb |
| BugReports | https://github.com/rorynolan/nandb/issues |
| LinkingTo | Rcpp (>= 1.0.1) |
| VignetteBuilder | knitr |
| Encoding | UTF-8 |
| Language | en-US |
| LazyData | TRUE |
| RoxygenNote | 7.1.0 |
| NeedsCompilation | yes |
| Packaged | 2020-05-08 03:37:09 UTC; rnolan |
| Repository | CRAN |
| Date/Publication | 2020-05-08 13:10:06 UTC |
| suggests | abind , covr , gridExtra , knitr , matrixStats (>= 0.50.0) , pacman , rmarkdown , spelling , testthat (>= 2.1.0) , tidyr |
| imports | assertthat , autothresholdr (>= 1.3.3) , BBmisc , checkmate (>= 1.9.3) , detrendr (>= 0.6.2) , dplyr , filesstrings (>= 3.1.5) , ggplot2 , glue (>= 1.3.0) , ijtiff (>= 2.0.2) , magrittr (>= 1.5) , purrr , Rcpp (>= 1.0.1) , reshape2 , rlang (>= 0.3.3) , stringr (>= 1.2.0) , utils , viridis , withr (>= 2.1.0) |
| depends | R (>= 3.1) |
| Contributors | Sergi Padilla-Parra, Luis Alvarez |
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