Package: frenchFISH 1.24.0

Adam Berman

frenchFISH: Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

Authors:Adam Berman, Geoff Macintyre

frenchFISH_1.24.0.tar.gz
frenchFISH_1.24.0.zip(r-4.7-any)frenchFISH_1.24.0.zip(r-4.6-any)frenchFISH_1.24.0.zip(r-4.5-any)
frenchFISH_1.24.0.tgz(r-4.6-any)frenchFISH_1.24.0.tgz(r-4.5-any)
frenchFISH_1.24.0.tar.gz(r-4.7-any)frenchFISH_1.24.0.tar.gz(r-4.6-any)
frenchFISH_1.24.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
frenchFISH/json (API)

# Install 'frenchFISH' in R:

install.packages('frenchFISH', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:frenchFISH-1.25.0(bioc 3.24)frenchFISH-1.24.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software biomedicalinformatics cellbiology genetics hiddenmarkovmodel preprocessing

4.00 score 5 scripts 268 downloads 3 exports 72 dependencies

Last updated from:344b49b9e9 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	169
linux-devel-x86_64	OK	200
source / vignettes	OK	220
linux-release-x86_64	OK	274
macos-release-arm64	OK	71
macos-oldrel-arm64	OK	81
windows-devel	OK	78
windows-release	OK	96
windows-oldrel	OK	80
wasm-release	OK	124

Exports:convertFishalyserCsvToCountMatrix getAutomaticCountsEstimates getManualCountsEstimates

Dependencies:abind backports boot broom car carData cli coda colorspace cowplot cpp11 Deriv doBy dplyr farver forecast Formula fracdiff generics ggplot2 glue gtable isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mcmc MCMCpack mgcv minqa modelr NHPoisson nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang S7 scales SparseM stringi stringr survival tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr zoo

Correcting FISH probe counts with frenchFISH

Adjusting automatically counted spots | Adjusting manually counted spots

Rendered fromfrenchFISH.Rmdusingknitr::rmarkdown

Last update: 2020-02-17
Started: 2020-02-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Helper function to check if all values in the input count matrix are either NA, NaN, or non-negative integers	areAllNonnegativeIntegers
Helper function to check the arguments input to getAutomaticCountsEstimates	checkAutomaticCountsEstimatesArguments
Helper function to check the arguments input to getManualCountsEstimates	checkManualCountsEstimatesArguments
Function to convert CSV output of the FISHalyseR automatic FISH splot counting software to a count matrix suitable for input to frenchFISH's getAutomaticCountsEstimates	convertFishalyserCsvToCountMatrix
Helper function to convert spot counts and nuclear area measurements into continuous events for Poisson point estimation	generatePPdat
FrenchFISH function for generating Poisson point estimates of spot counts from spot counts which have been automatically generated.	getAutomaticCountsEstimates
Helper function to get the average volume of nucleus sampled given the nucleus radius and section height	getAverageVolumeFrac
FrenchFISH function for generating volume adjusted spot counts from spots which have been manually counted (uses a Markov chain Monte Carlo method).	getManualCountsEstimates
Helper function to get the maximum possible volume of nucleus sampled given the nucleus radius and section height	getMaxVolumeFrac
Helper function that returns the minimum possible volume of nucleus sampled given the nucleus radius and section height	getMinVolumeFrac
Helper function that returns the fraction of the nucleus sampled for a specified distance from the midpoint	getVsegFrac