Files in rorynolan/nandb
Number and Brightness Image Analysis
.DS_Store
.Rbuildignore
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
.pre-commit-config.yaml
.travis.yml
CONDUCT.md
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/.DS_Store
R/RcppExports.R
R/brightness.R
R/cc_brightness.R
R/cc_number.R
R/class_constructors.R
R/cross_var.R
R/graphics.R
R/nandb-package.R
R/number.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
appveyor.yml
codecov.yml
codemeta.json
cran-comments.md
index.Rmd
index.md
inst/.DS_Store
inst/CITATION
inst/WORDLIST
inst/extdata/50.tif
inst/extdata/50_big.tif
inst/extdata/b.bin
inst/extdata/needs_rescaling.tif
inst/extdata/two_ch.tif
junk/AdaptiveDetrend.Rmd
junk/detrend.R
junk/graphics.R
junk/intensity.R
junk/kmers.R
junk/movement.R
junk/movement.cc
junk/nandb.png
junk/possibleJunk.R
junk/possibleJunk.cpp
junk/sticker.R
junk/sticker.png
junk/test_detrend.R
junk/test_graphics.R
junk/test_intensity.R
junk/test_io.R
junk/test_kmers.R
junk/utils.cc
man/brightness.Rd
man/brightness_folder.Rd
man/brightness_timeseries.Rd
man/brightness_timeseries_folder.Rd
man/cc-nb-img-classes.Rd
man/cc-nb-ts-img-classes.Rd
man/cc_brightness.Rd
man/cc_brightness_folder.Rd
man/cc_brightness_timeseries.Rd
man/cc_brightness_timeseries_folder.Rd
man/cc_number.Rd
man/cc_number_folder.Rd
man/cc_number_timeseries.Rd
man/cc_number_timeseries_folder.Rd
man/cross_var.Rd
man/cross_var_pillars.Rd
man/figures/logo.png
man/matrix_raster_plot.Rd
man/median_filter.Rd
man/nandb.Rd
man/nb-img-classes.Rd
man/nb-ts-img-classes.Rd
man/number.Rd
man/number_folder.Rd
man/number_timeseries.Rd
man/number_timeseries_folder.Rd
nandb.Rproj
paper_data/.DS_Store
paper_data/bleachvis/bleachvis.R
paper_data/bleachvis/bleachvis.Rproj
paper_data/bleachvis/bleachvis1.pdf
paper_data/bleachvis/bleachvis2.pdf
paper_data/bleachvis/main_before.tif
paper_data/edges/dontbenaive.pdf
paper_data/edges/edges.R
paper_data/edges/edges.Rproj
paper_data/fkbp/.DS_Store
paper_data/fkbp/bleachvis1.pdf
paper_data/fkbp/bleachvis2.pdf
paper_data/fkbp/compareconcs.pdf
paper_data/fkbp/decays.pdf
paper_data/fkbp/fkbp.R
paper_data/fkbp/fkbp.Rproj
paper_data/fkbp/fold_changes_cells.csv
paper_data/fkbp/fold_changes_sum.csv
paper_data/fkbp/foldchanges.pdf
paper_data/fkbp/master.csv
paper_data/fkbp/well1_cell1_after_25nM - C1.tif
paper_data/fkbp/well1_cell1_after_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell1_after_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell1_after_25nM - C1_brightness_frames=50_tau=auto=162_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell1_before_25nM - C1.tif
paper_data/fkbp/well1_cell1_before_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell1_before_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell1_before_25nM - C1_brightness_frames=50_tau=auto=98_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell2_after_25nM - C1.tif
paper_data/fkbp/well1_cell2_after_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell2_after_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell2_after_25nM - C1_brightness_frames=50_tau=auto=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell2_before_25nM - C1.tif
paper_data/fkbp/well1_cell2_before_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell2_before_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell2_before_25nM - C1_brightness_frames=50_tau=auto=160_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell3_after_25nM - C1.tif
paper_data/fkbp/well1_cell3_after_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell3_after_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell3_after_25nM - C1_brightness_frames=50_tau=auto=189_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell3_before_25nM - C1.tif
paper_data/fkbp/well1_cell3_before_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell3_before_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell3_before_25nM - C1_brightness_frames=50_tau=auto=269_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell4_after_25nM - C1.tif
paper_data/fkbp/well1_cell4_after_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell4_after_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell4_after_25nM - C1_brightness_frames=50_tau=auto=126_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell4_before_25nM - C1.tif
paper_data/fkbp/well1_cell4_before_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell4_before_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell4_before_25nM - C1_brightness_frames=50_tau=auto=142_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell5_after_25nM - C1.tif
paper_data/fkbp/well1_cell5_after_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell5_after_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell5_after_25nM - C1_brightness_frames=50_tau=auto=150_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell5_before_25nM - C1.tif
paper_data/fkbp/well1_cell5_before_25nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell5_before_25nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well1_cell5_before_25nM - C1_brightness_frames=50_tau=auto=102_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell1_after_12.5nM - C1.tif
paper_data/fkbp/well2_cell1_after_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell1_after_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell1_after_12.5nM - C1_brightness_frames=50_tau=auto=188_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell1_before_12.5nM - C1.tif
paper_data/fkbp/well2_cell1_before_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell1_before_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell1_before_12.5nM - C1_brightness_frames=50_tau=auto=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell2_after_12.5nM - C1.tif
paper_data/fkbp/well2_cell2_after_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell2_after_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell2_after_12.5nM - C1_brightness_frames=50_tau=auto=140_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell2_before_12.5nM - C1.tif
paper_data/fkbp/well2_cell2_before_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell2_before_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell2_before_12.5nM - C1_brightness_frames=50_tau=auto=78_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell3_after_12.5nM - C1.tif
paper_data/fkbp/well2_cell3_after_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell3_after_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell3_after_12.5nM - C1_brightness_frames=50_tau=auto=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell3_before_12.5nM - C1.tif
paper_data/fkbp/well2_cell3_before_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell3_before_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell3_before_12.5nM - C1_brightness_frames=50_tau=auto=123_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell4_after_12.5nM - C1.tif
paper_data/fkbp/well2_cell4_after_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell4_after_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell4_after_12.5nM - C1_brightness_frames=50_tau=auto=138_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell4_before_12.5nM - C1.tif
paper_data/fkbp/well2_cell4_before_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell4_before_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell4_before_12.5nM - C1_brightness_frames=50_tau=auto=105_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell5_after_12.5nM - C1.tif
paper_data/fkbp/well2_cell5_after_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell5_after_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell5_after_12.5nM - C1_brightness_frames=50_tau=auto=136_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell5_before_12.5nM - C1.tif
paper_data/fkbp/well2_cell5_before_12.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell5_before_12.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well2_cell5_before_12.5nM - C1_brightness_frames=50_tau=auto=128_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell1_after_5nM - C1.tif
paper_data/fkbp/well3_cell1_after_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell1_after_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell1_after_5nM - C1_brightness_frames=50_tau=auto=143_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell1_before_5nM - C1.tif
paper_data/fkbp/well3_cell1_before_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell1_before_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell1_before_5nM - C1_brightness_frames=50_tau=auto=93_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell2_after_5nM - C1.tif
paper_data/fkbp/well3_cell2_after_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell2_after_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell2_after_5nM - C1_brightness_frames=50_tau=auto=170_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell2_before_5nM - C1.tif
paper_data/fkbp/well3_cell2_before_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell2_before_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell2_before_5nM - C1_brightness_frames=50_tau=auto=129_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell3_after_5nM - C1.tif
paper_data/fkbp/well3_cell3_after_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell3_after_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell3_after_5nM - C1_brightness_frames=50_tau=auto=88_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell3_before_5nM - C1.tif
paper_data/fkbp/well3_cell3_before_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell3_before_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell3_before_5nM - C1_brightness_frames=50_tau=auto=133_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell4_after_5nM - C1.tif
paper_data/fkbp/well3_cell4_after_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell4_after_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell4_after_5nM - C1_brightness_frames=50_tau=auto=186_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell4_before_5nM - C1.tif
paper_data/fkbp/well3_cell4_before_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell4_before_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell4_before_5nM - C1_brightness_frames=50_tau=auto=91_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell5_after_5nM - C1.tif
paper_data/fkbp/well3_cell5_after_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell5_after_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell5_after_5nM - C1_brightness_frames=50_tau=auto=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell5_before_5nM - C1.tif
paper_data/fkbp/well3_cell5_before_5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell5_before_5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well3_cell5_before_5nM - C1_brightness_frames=50_tau=auto=111_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell1_after_0.5nM - C1.tif
paper_data/fkbp/well4_cell1_after_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell1_after_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell1_after_0.5nM - C1_brightness_frames=50_tau=auto=122_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell1_before_0.5nM - C1.tif
paper_data/fkbp/well4_cell1_before_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell1_before_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell1_before_0.5nM - C1_brightness_frames=50_tau=auto=121_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell2_after_0.5nM - C1.tif
paper_data/fkbp/well4_cell2_after_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell2_after_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell2_after_0.5nM - C1_brightness_frames=50_tau=auto=124_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell2_before_0.5nM - C1.tif
paper_data/fkbp/well4_cell2_before_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell2_before_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell2_before_0.5nM - C1_brightness_frames=50_tau=auto=72_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell3_after_0.5nM - C1.tif
paper_data/fkbp/well4_cell3_after_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell3_after_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell3_after_0.5nM - C1_brightness_frames=50_tau=auto=144_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell3_before_0.5nM - C1.tif
paper_data/fkbp/well4_cell3_before_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell3_before_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell3_before_0.5nM - C1_brightness_frames=50_tau=auto=130_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell4_after_0.5nM - C1.tif
paper_data/fkbp/well4_cell4_after_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell4_after_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell4_after_0.5nM - C1_brightness_frames=50_tau=auto=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell4_before_0.5nM - C1.tif
paper_data/fkbp/well4_cell4_before_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell4_before_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell4_before_0.5nM - C1_brightness_frames=50_tau=auto=176_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell5_after_0.5nM - C1.tif
paper_data/fkbp/well4_cell5_after_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell5_after_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell5_after_0.5nM - C1_brightness_frames=50_tau=auto=221_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell5_before_0.5nM - C1.tif
paper_data/fkbp/well4_cell5_before_0.5nM - C1_brightness_frames=50_tau=10_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell5_before_0.5nM - C1_brightness_frames=50_tau=NA_mst=MinError_filter=NA.csv
paper_data/fkbp/well4_cell5_before_0.5nM - C1_brightness_frames=50_tau=auto=142_mst=MinError_filter=NA.csv
paper_data/mainfig/main_before.tif
paper_data/mainfig/main_with.tif
paper_data/mainfig/mainfig.R
paper_data/mainfig/mainfig.Rproj
paper_data/sim/.DS_Store
paper_data/sim/Simulation01M_rep1.tif
paper_data/sim/Simulation01M_rep1_bleach=exponential0.5.tif
paper_data/sim/Simulation01M_rep1_bleach=exponential0.5_brightness_frames=500_tau=10_mst=NA_filter=NA.csv
paper_data/sim/Simulation01M_rep1_bleach=exponential0.5_brightness_frames=500_tau=NA_mst=NA_filter=NA.csv
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