Package: nandb 2.1.0

nandb: 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>.

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

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nandb.pdf |nandb.html✨
nandb/json (API)
NEWS

# Install 'nandb' in R:
install.packages('nandb', repos = c('https://rorynolan.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rorynolan/nandb/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

5.24 score 2 stars 29 scripts 280 downloads 2 mentions 29 exports 69 dependencies

Last updated 3 years agofrom:43ad4ee009. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-win-x86_64OKNov 03 2024
R-4.5-linux-x86_64OKNov 03 2024
R-4.4-win-x86_64OKNov 03 2024
R-4.4-mac-x86_64OKNov 03 2024
R-4.4-mac-aarch64OKNov 03 2024
R-4.3-win-x86_64OKNov 03 2024
R-4.3-mac-x86_64OKNov 03 2024
R-4.3-mac-aarch64OKNov 03 2024

Exports:brightnessbrightness_folderbrightness_imgbrightness_timeseriesbrightness_timeseries_folderbrightness_ts_imgcc_brightnesscc_brightness_foldercc_brightness_imgcc_brightness_timeseriescc_brightness_timeseries_foldercc_brightness_ts_imgcc_numbercc_number_foldercc_number_imgcc_number_timeseriescc_number_timeseries_foldercc_number_ts_imgcross_varcross_var_pillarsmatrix_raster_plotmedian_filternumbernumber_foldernumber_imgnumber_timeseriesnumber_timeseries_foldernumber_ts_imgsmooth_filter

Dependencies:arrayhelpersassertthatautothresholdrbackportsBBmiscbitbit64checkmateclicliprcodetoolscolorspacecpp11crayondata.tabledetrendrdoParalleldplyrfansifarverfilesstringsforeachfsgenericsggplot2gluegridExtragtablehmsijtiffisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppRcppParallelreadrreshape2rlangscalesstrexstringistringrsvUnittibbletidyselecttzdbutf8vctrsviridisviridisLitevroomwithrzeallot

Batch mode

Rendered frombatch-mode.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2018-10-30
Started: 2018-10-30

Brightness timeseries

Rendered frombrightness-timeseries.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2018-10-30
Started: 2018-10-30

Calculating brightness with single images

Rory Nolan

Rendered fromsingle-images.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2019-05-21
Started: 2018-10-30

Readme and manuals

Help Manual

Help pageTopics
Calculate brightness from image series.brightness
Brightness calculations for every image in a folder.brightness_folder
Create a brightness time-series.brightness_timeseries
Brightness time-series calculations for every image in a folder.brightness_timeseries_folder
Cross-correlated brightness.cc_brightness
Cross-correlated brightness calculations for every image in a folder.cc_brightness_folder
Create a cross-correlated brightness time-series.cc_brightness_timeseries
Cross-correlated brightness time-series calculations for every image in a folder.cc_brightness_timeseries_folder
Cross-correlated number.cc_number
Cross-correlated number calculations for every image in a folder.cc_number_folder
Create a cross-correlated number time-series.cc_number_timeseries
Cross-correlated number time-series calculations for every image in a folder.cc_number_timeseries_folder
Cross-correlated number and brightness image classes.cc-nb-img-classes cc_brightness_img cc_number_img
Cross-correlated number and brightness time series image classes.cc-nb-ts-img-classes cc_brightness_ts_img cc_number_ts_img
Calculate the _cross-variance_ of two vectors.cross_var
Calculate the _cross-variance_ of corresponding pillars of 3d arrays.cross_var_pillars
Make a raster plot of a matrix.matrix_raster_plot
Smooth and median filters with options for handling NAs.median_filter smooth_filter
nandb: Number and brightness in R.nandb-package nandb
Number and brightness image classes.brightness_img nb-img-classes number_img
Number and brightness time series image classes.brightness_ts_img nb-ts-img-classes number_ts_img
Calculate number from image series.number
Number calculations for every image in a folder.number_folder
Create a number time-series.number_timeseries
Number time-series calculations for every image in a folder.number_timeseries_folder