Package: CB2 1.3.4

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_1.3.4.tar.gz
CB2_1.3.4.tar.gz(r-4.5-noble)CB2_1.3.4.tar.gz(r-4.4-noble)
CB2_1.3.4.tgz(r-4.4-emscripten)CB2_1.3.4.tgz(r-4.3-emscripten)
CB2.pdf |CB2.html
CB2/json (API)

# Install 'CB2' in R:
install.packages('CB2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

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

3.60 score 40 scripts 290 downloads 1 mentions 13 exports 78 dependencies

Last updated 4 years agofrom:b32975d586. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-linux-x86_64NOTEOct 28 2024

Exports:calc_mappabilityfit_abget_CPMjoin_count_and_designmeasure_gene_statsmeasure_sgrna_statsplot_corr_heatmapplot_count_distributionplot_dotplotplot_PCAquantrun_estimationrun_sgrna_quant

Dependencies:BiobaseBiocGenericsbitbit64clicliprcodetoolscolorspacecpp11crayonDEoptimRdplyrfansifarvergenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSmathjaxrMatrixMatrixModelsmetapmgcvmnormtmultcompmulttestmunsellmutossmvtnormnlmenumDerivpheatmappillarpkgconfigplotrixprettyunitsprogresspurrrqqconfquantregR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRdpackreadrrlangrobustbasesandwichscalessnSparseMstringistringrsurvivalTFisherTH.datatibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrzoo

CB2 Tutorial

Rendered fromcb2-tutorial.Rmdusingknitr::rmarkdownon Oct 28 2024.

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

Handling the input matrix in CB2

Rendered fromcb2-input-handling.Rmdusingknitr::rmarkdownon Oct 28 2024.

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