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'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

Evers_CRISPRn_RT112 - A benchmark CRISPRn pooled screen data from Evers et al.
Sanson_CRISPRn_A375 - A benchmark CRISPRn pooled screen data from Sanson et al.

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

cpp

3.60 score 40 scripts 303 downloads 1 mentions 13 exports 78 dependencies

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

Target	Result	Date
Doc / Vignettes	OK	Nov 27 2024
R-4.5-linux-x86_64	NOTE	Nov 27 2024

Exports:calc_mappability fit_ab get_CPM join_count_and_design measure_gene_stats measure_sgrna_stats plot_corr_heatmap plot_count_distribution plot_dotplot plot_PCA quant run_estimation run_sgrna_quant

Dependencies:Biobase BiocGenerics bit bit64 cli clipr codetools colorspace cpp11 crayon DEoptimR dplyr fansi farver generics ggplot2 glue gtable hms isoband labeling lattice lifecycle magrittr MASS mathjaxr Matrix MatrixModels metap mgcv mnormt multcomp multtest munsell mutoss mvtnorm nlme numDeriv pheatmap pillar pkgconfig plotrix prettyunits progress purrr qqconf quantreg R.methodsS3 R.oo R.utils R6 rbibutils RColorBrewer Rcpp RcppArmadillo Rdpack readr rlang robustbase sandwich scales sn SparseM stringi stringr survival TFisher TH.data tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr zoo

CB2 Tutorial

Hyun-Hwan Jeong

Rendered fromcb2-tutorial.Rmdusingknitr::rmarkdownon Nov 27 2024.

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

Handling the input matrix in CB2

Hyun-Hwan Jeong

Rendered fromcb2-input-handling.Rmdusingknitr::rmarkdownon Nov 27 2024.

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

Citation

Readme and manuals

Help Manual

Help page	Topics
A function to calculate the mappabilities of each NGS sample.	calc_mappability
A benchmark CRISPRn pooled screen data from Evers et al.	Evers_CRISPRn_RT112
A C++ function to perform a parameter estimation for the sgRNA-level test. It will estimate two different parameters `phat` and `vhat,` and we assume input count data follows the beta-binomial distribution. Dr. Keith Baggerly initially implemented this code in Matlab, and it has been rewritten it in C++ for the speed-up.	fit_ab
A function to normalize sgRNA read counts.	get_CPM
A function to join a count table and a design table.	join_count_and_design
A function to perform gene-level test using a sgRNA-level statistics.	measure_gene_stats
A function to perform a statistical test at a sgRNA-level	measure_sgrna_stats
A function to show a heatmap sgRNA-level corrleations of the NGS samples.	plot_corr_heatmap
A function to plot read count distribution.	plot_count_distribution
A function to visualize dot plots for a gene.	plot_dotplot
A function to plot the first two principal components of samples.	plot_PCA
A C++ function to quantify sgRNA abundance from NGS samples.	quant
A function to perform a statistical test at a sgRNA-level, deprecated.	run_estimation
A function to run a sgRNA quantification algorithm from NGS sample	run_sgrna_quant
A benchmark CRISPRn pooled screen data from Sanson et al.	Sanson_CRISPRn_A375

Package: CB2 1.3.4

CB2: CRISPR Pooled Screen Analysis using Beta-Binomial Test

CB2 Tutorial

Handling the input matrix in CB2

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)