Package: CB2 1.3.8

Hyun-Hwan Jeong

CB2: CRISPR Pooled Screen Analysis using Beta-Binomial Test

Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.

Authors:Hyun-Hwan Jeong [aut, cre]

CB2_1.3.8.tar.gz
CB2_1.3.8.tar.gz(r-4.7-arm64)CB2_1.3.8.tar.gz(r-4.7-x86_64)CB2_1.3.8.tar.gz(r-4.6-arm64)CB2_1.3.8.tar.gz(r-4.6-x86_64)
CB2_1.3.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CB2/json (API)

# Install 'CB2' in R:
install.packages('CB2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

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

cpp

3.92 score 42 scripts 431 downloads 1 mentions 14 exports 74 dependencies

Last updated from:f62732a533. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK163
linux-devel-x86_64OK172
source / vignettesOK262
linux-release-arm64OK177
linux-release-x86_64OK173
wasm-releaseOK175

Exports:calc_mappabilityfit_abget_CPMjoin_count_and_designmeasure_gene_statsmeasure_sgrna_statsplot_corr_heatmapplot_count_distributionplot_dotplotplot_PCAquantrep_rowrun_estimationrun_sgrna_quant

Dependencies:BiobaseBiocGenericsbitbit64clicliprcodetoolscpp11crayonDEoptimRdplyrfarvergenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSmathjaxrMatrixMatrixModelsmetapmnormtmultcompmulttestmutossmvtnormnumDerivpheatmappillarpkgconfigplotrixprettyunitsprogresspurrrqqconfquantregR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRdpackreadrrlangrobustbaseS7sandwichscalessnSparseMstringistringrsurvivalTFisherTH.datatibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrzoo

CB2 Tutorial
Rendered fromcb2-tutorial.Rmdusingknitr::rmarkdown

Last update: 2020-05-12
Started: 2019-02-11

Handling the input matrix in CB2
References
Rendered fromcb2-input-handling.Rmdusingknitr::rmarkdown

Last update: 2020-04-15
Started: 2019-12-17