Package: CONFESS 1.41.0

Diana LOW

CONFESS: Cell OrderiNg by FluorEScence Signal

Single Cell Fluidigm Spot Detector.

Authors:Diana LOW and Efthimios MOTAKIS

CONFESS_1.41.0.tar.gz
CONFESS_1.41.0.zip(r-4.7)CONFESS_1.41.0.zip(r-4.6)CONFESS_1.41.0.zip(r-4.5)
CONFESS_1.41.0.tgz(r-4.6-any)CONFESS_1.41.0.tgz(r-4.5-any)
CONFESS_1.41.0.tar.gz(r-4.7-any)CONFESS_1.41.0.tar.gz(r-4.6-any)
CONFESS_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CONFESS/json (API)

# Install 'CONFESS' in R:

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

Datasets:

clu - Clu
estimates - Estimates
estimates.2 - Estimates.2
files - Files
Results - Results
step1 - Step1
step2 - Step2
step2.1 - Step2.1
step3 - Step3
step3.1 - Step3.1
step4 - Step4
steps2_4 - Steps2_4

On BioConductor:CONFESS-1.41.0(bioc 3.24)CONFESS-1.40.0(bioc 3.23)

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

immunooncology geneexpression dataimport cellbiology clustering rnaseq qualitycontrol visualization timecourse regression classification

3.90 score 3 scripts 2 mentions 17 exports 139 dependencies

Last updated from:fa0d855106. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	274
linux-devel-x86_64	WARNING	642
source / vignettes	OK	488
linux-release-x86_64	WARNING	636
macos-release-arm64	WARNING	341
macos-oldrel-arm64	WARNING	276
windows-devel	WARNING	390
windows-release	WARNING	407
windows-oldrel	WARNING	401
wasm-release	OK	241

Exports:cluster2outlier createFluo defineLocClusters Fluo_adjustment Fluo_CV_modeling Fluo_CV_prep Fluo_inspection Fluo_modeling Fluo_ordering FluoSelection_byRun getFluo getFluo_byRun LocationMatrix pathEstimator readFiles simcells spotEstimator

Dependencies:abind backports base64enc BH Biobase BiocGenerics biocmake bitops bmp bslib cachem changepoint checkmate cli cluster codetools colorspace contrast cpp11 cytolib data.table DEoptimR digest dir.expiry EBImage ecp evaluate farver fastmap feature fftwtools filelock flexmix flowClust flowCore flowMeans flowMerge flowPeaks FNN fontawesome foreach foreign Formula fs generics ggplot2 glue graph gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets isoband iterators jpeg jquerylib jsonlite kernlab KernSmooth knitr ks labeling lattice lifecycle limma locfit magrittr MASS Matrix MatrixModels matrixStats mclust memoise mgcv mime misc3d modeltools moments multcomp multicool multitaper mvtnorm nlme nnet outliers pcaPP plot3D plotrix plyr png polspline pracma quantreg R6 rappdirs raster RColorBrewer Rcpp RCurl readbitmap reshape2 Rgraphviz Rhdf5lib rlang rmarkdown rms robustbase rpart RProtoBufLib rrcov rstudioapi S4Vectors S7 SamSPECTRAL sandwich sass scales snow sp SparseM statmod stringi stringr survival terra TH.data tiff tinytex vctrs viridisLite waveslim wavethresh withr xfun yaml zoo

Preliminaries | Loading the packages | Data pre-processing | Fluorescence estimation | Reading in image/text files | Image spot estimation | Quality control (identification of outliers) | Re-estimation step (for outliers) | Final estimation | Fluorescence adjustment and estimation of cell cycle phases / pseudotime | Fluorescence adjustment on estimations from Section 2.6 | Data inspection by batch (chip) | If data consists of more than 1 chip run/batch | If data consists of a single chip run/batch | Cross-validation to assess the stability of the estimates

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2019-02-26
Started: 2016-03-29

1 Preliminaries | 2 Fluorescence estimation | 3 Adjustment and estimation of cell cycle phases / pseudotime

Rendered fromvignette_tex.Rnwusingknitr::knitr

Last update: 2016-04-11
Started: 2016-03-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
clu	clu
cluster2outlier	cluster2outlier
createFluo	createFluo
defineLocClusters	defineLocClusters
estimates	estimates
estimates.2	estimates.2
files	files
Fluo_adjustment	Fluo_adjustment
Fluo_CV_modeling	Fluo_CV_modeling
Fluo_CV_prep	Fluo_CV_prep
Fluo_inspection	Fluo_inspection
Fluo_modeling	Fluo_modeling
Fluo_ordering	Fluo_ordering
FluoSelection_byRun	FluoSelection_byRun
getFluo	getFluo
getFluo_byRun	getFluo_byRun
LocationMatrix	LocationMatrix
pathEstimator	pathEstimator
readFiles	readFiles
Results	Results
simcells	simcells
spotEstimator	spotEstimator
step1	step1
step2	step2
step2.1	step2.1
step3	step3
step3.1	step3.1
step4	step4
steps2_4	steps2_4

Usage by other packages (reverse dependencies)