Package: gscreend 1.21.0

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_1.21.0.tar.gz
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gscreend.pdf |gscreend.html✨
gscreend/json (API)
NEWS

# 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-1.19.0(bioc 3.20)gscreend-1.18.0(bioc 3.19)

software statisticalmethod pooledscreens crispr

6.34 score 11 stars 7 scripts 138 downloads 2 mentions 7 exports 51 dependencies

Last updated 23 days agofrom:12b0796e3c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:createPoolScreenExp GeneData plotModelParameters plotReplicateCorrelation ResultsTable RunGscreend sgRNAData

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel codetools cpp11 crayon curl cvar DelayedArray fastICA fBasics fGarch formatR futile.logger futile.options gbutils GenomeInfoDb GenomeInfoDbData GenomicRanges gss httr IRanges jsonlite lambda.r lattice MASS Matrix MatrixGenerics matrixStats mime nloptr openssl R6 rbibutils Rdpack S4Arrays S4Vectors snow SparseArray spatial stabledist SummarizedExperiment sys timeDate timeSeries UCSC.utils XVector zlibbioc

Vignette illustrating the usage of gscreend on simulated data

Katharina Imkeller

Rendered fromgscreend_simulated_data.Rmdusingknitr::rmarkdownon Oct 30 2024.

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