strex - Extra String Manipulation Functions

There are some things that I wish were easier with the 'stringr' or 'stringi' packages. The foremost of these is the extraction of numbers from strings. 'stringr' and 'stringi' make you figure out the regular expression for yourself; 'strex' takes care of this for you. There are many other handy functionalities in 'strex'. Contributions to this package are encouraged; it is intended as a miscellany of string manipulation functions that cannot be found in 'stringi' or 'stringr'.

Last updated 5 months ago

10.79 score 41 stars 18 dependents 1.2k scripts 2.0k downloads

ijtiff - Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.net/ij/>. Also supports text image I/O.

Last updated 4 hours ago

image-manipulationimagejpeer-reviewedtiff-filestiff-imagestiff

8.47 score 18 stars 7 dependents 36 scripts 1.6k downloads

filesstrings - Handy File and String Manipulation

This started out as a package for file and string manipulation. Since then, the 'fs' and 'strex' packages emerged, offering functionality previously given by this package (but it's done better in these new ones). Those packages have hence almost pushed 'filesstrings' into extinction. However, it still has a small number of unique, handy file manipulation functions which can be seen in the vignette. One example is a function to remove spaces from all file names in a directory.

Last updated 1 years ago

8.46 score 22 stars 4 dependents 644 scripts 1.1k downloads

autothresholdr - An R Port of the 'ImageJ' Plugin 'Auto Threshold'

Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <https://imagej.net/plugins/auto-threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.

Last updated 1 years ago

cpp

6.61 score 6 stars 4 dependents 31 scripts 1.2k downloads

exampletestr - Help for Writing Unit Tests Based on Function Examples

Take the examples written in your documentation of functions and use them to create shells (skeletons which must be manually completed by the user) of test files to be tested with the 'testthat' package. Sort of like python 'doctests' for R.

Last updated 4 months ago

6.53 score 38 stars 8 scripts 983 downloads

detrendr - Detrend Images

Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This package contains functionality published in a 2016 paper <doi:10.1093/bioinformatics/btx434> but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.

Last updated 22 days ago

cpp

6.02 score 3 stars 1 dependents 26 scripts 894 downloads

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>.

Last updated 22 days ago

cpp

5.24 score 2 stars 29 scripts 362 downloads