Package: gscreend 1.27.0

Katharina Imkeller

gscreend: Analysis of pooled genetic screens

Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.

Authors:Katharina Imkeller [cre, aut], Wolfgang Huber [aut]

gscreend_1.27.0.tar.gz
gscreend_1.27.0.zip(r-4.7)gscreend_1.27.0.zip(r-4.6)gscreend_1.27.0.zip(r-4.5)
gscreend_1.27.0.tgz(r-4.6-any)gscreend_1.27.0.tgz(r-4.5-any)
gscreend_1.27.0.tar.gz(r-4.7-any)gscreend_1.27.0.tar.gz(r-4.6-any)
gscreend_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gscreend/json (API)

# Install 'gscreend' in R:

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

Bug tracker:https://github.com/imkeller/gscreend/issues

On BioConductor:gscreend-1.27.0(bioc 3.24)gscreend-1.26.0(bioc 3.23)

software statisticalmethod pooledscreens crispr

6.08 score 12 stars 8 scripts 2 mentions 7 exports 40 dependencies

Last updated from:b8621dfc5a. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	177
linux-devel-x86_64	OK	366
source / vignettes	OK	285
linux-release-x86_64	OK	336
macos-release-arm64	OK	171
macos-oldrel-arm64	OK	211
windows-devel	OK	293
windows-release	OK	297
windows-oldrel	OK	274
wasm-release	OK	142

Exports:createPoolScreenExp GeneData plotModelParameters plotReplicateCorrelation ResultsTable RunGscreend sgRNAData

Dependencies:abind BH Biobase BiocGenerics BiocParallel codetools cpp11 cvar DelayedArray fastICA fBasics fGarch formatR futile.logger futile.options gbutils generics GenomicRanges gss IRanges lambda.r lattice MASS Matrix MatrixGenerics matrixStats nloptr rbibutils Rdpack S4Arrays S4Vectors Seqinfo snow SparseArray spatial stabledist SummarizedExperiment timeDate timeSeries XVector

Vignette illustrating the usage of gscreend on simulated data

Rendered fromgscreend_simulated_data.Rmdusingknitr::rmarkdown

Last update: 2021-08-09
Started: 2019-07-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create PoolScreenExp Experiment	createPoolScreenExp
GeneData: set and retrieve GeneData of PoolScreenExp	GeneData
Accessor function for the Gene slot of the PoolScreenExp class	GeneData,PoolScreenExp-method
Plot model parameters from the fitting	plotModelParameters
Plot replicate correlation	plotReplicateCorrelation
Class to store pooled CRISPR screening experiment	PoolScreenExp-class
Extract a results table	ResultsTable
run gscreend	RunGscreend
sgRNAData: set and retrieve sgRNAData of PoolScreenExp	sgRNAData
Accessor function for the sgRNA slot of the PoolScreenExp class	sgRNAData,PoolScreenExp-method