detrendr v0.6.12
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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unpublished work.
Readme
detrendr 
Detrend fluorescence microscopy image series for fluorescence fluctuation and correlation spectroscopy (FCS and FFS) analysis. This package contains functionality published in a 2016 paper https://doi.org/10.1093/bioinformatics/btx434 but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.
Installation
You can install the release version of detrendr from
CRAN with:
install.packages("detrendr")
You can install the (unstable) development version of detrendr from
GitHub with:
devtools::install_github("rorynolan/detrendr")
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/detrendr/.
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 detrendr
| Name | Description | |
| best_tau | Find the best tau parameter for exponential smoothing detrending. | |
| best_degree | Find the best polynomial degree for polynomial detrending. | |
| apply_on_pillars | Apply a function to each pillar of a 3-dimensional array. | |
| detrended_img | Detrended image class. | |
| best_l | Find the best length parameter for boxcar detrending. | |
| detrend-directory | Detrend all TIFF images in an entire folder. | |
| detrending | Detrend images. | |
| best_swaps | Find the best swaps parameter for Robin Hood detrending. | |
| detrendr | detrendr: Image detrending in R. | |
| mean_frames | Get the sums/means of frames in a 3-dimensional array. | |
| brightness_pillars | Get the brightness of pillars of a 3d array. | |
| pillar-stats | Get the sums/means/medians/variances of pillars of an ijtiff_img-style array. | |
| rfromboxes | Randomly draw balls from boxes. | |
| rtoboxes | Randomly place balls in boxes. | |
| No Results! | ||
Vignettes of detrendr
| Name | ||
| batch-mode.Rmd | ||
| linescan-data.Rmd | ||
| single-images.Rmd | ||
| No Results! | ||
Last month downloads
Details
| Type | Package |
| License | BSD_3_clause + file LICENSE |
| URL | https://rorynolan.github.io/detrendr/, https://github.com/rorynolan/detrendr#readme |
| BugReports | https://github.com/rorynolan/detrendr/issues |
| LinkingTo | Rcpp (>= 1.0.1), RcppParallel (>= 5.0.2) |
| VignetteBuilder | knitr |
| Encoding | UTF-8 |
| Language | en-US |
| LazyData | true |
| RoxygenNote | 7.1.1 |
| SystemRequirements | GNU make |
| NeedsCompilation | yes |
| Packaged | 2021-02-08 04:51:06 UTC; rnolan |
| Repository | CRAN |
| Date/Publication | 2021-02-08 06:00:03 UTC |
| suggests | abind , covr , ggplot2 , glue (>= 1.3.0) , graphics , gridExtra , knitr , lattice , MASS , matrixStats , mgcv , pacman , R.utils , rmarkdown , spelling , testthat , tidyr |
| imports | arrayhelpers (>= 1.1.0) , autothresholdr (>= 1.3.7) , checkmate (>= 1.9.3) , doParallel , dplyr , filesstrings (>= 3.2) , foreach , ijtiff (>= 2.2) , iterators , magrittr (>= 1.5) , parallel , plyr , purrr , Rcpp (>= 1.0.1) , RcppParallel (>= 5.0.2) , rlang (>= 0.3.3) , stringr (>= 1.4) , tools , withr (>= 2.1) |
| depends | R (>= 3.1) |
| Contributors | Sergi Padilla-Parra, Luis Alvarez |
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