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 but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.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but it has been extended since then with the Robin Hood algorithm and thus contains unpublished work.

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Project Status: Active – The project has reached a stable, usable
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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.
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Vignettes of detrendr

Name
batch-mode.Rmd
linescan-data.Rmd
single-images.Rmd
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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

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