Package: MAGeCKFlute
Type: Package
Title: Integrative Analysis Pipeline for Pooled CRISPR Functional
        Genetic Screens
Version: 2.0.0
Date: "`r Sys.Date()`"
Author: Binbin Wang, Wubing Zhang, Feizhen Wu, Wei Li & X. Shirley Liu
Maintainer: Wubing Zhang <Watson5bZhang@gmail.com>
Description: CRISPR (clustered regularly interspaced short palindrome repeats) coupled 
  with nuclease Cas9 (CRISPR/Cas9) screens represent a promising technology to 
  systematically evaluate gene functions. Data analysis for CRISPR/Cas9 screens is a 
  critical process that includes identifying screen hits and exploring biological functions 
  for these hits in downstream analysis. We have previously developed two algorithms, 
  MAGeCK and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various scenarios. 
  These two algorithms allow users to perform quality control, read count generation and 
  normalization, and calculate beta score to evaluate gene selection performance. 
  In downstream analysis, the biological functional analysis is required for understanding 
  biological functions of these identified genes with different screening purposes. 
  Here, We developed MAGeCKFlute for supporting downstream analysis. MAGeCKFlute provides 
  several strategies to remove potential biases within sgRNA-level read counts and 
  gene-level beta scores. The downstream analysis with the package includes identifying 
  essential, non-essential, and target-associated genes, and performing biological 
  functional category analysis, pathway enrichment analysis and protein complex enrichment 
  analysis of these genes. The package also visualizes genes in multiple ways to benefit 
  users exploring screening data. Collectively, MAGeCKFlute enables accurate identification 
  of essential, non-essential, and targeted genes, as well as their related biological 
  functions. This vignette explains the use of the package and demonstrates typical workflows.
License: GPL (>=3)
VignetteBuilder: knitr
Depends: R (>= 4.1)
Imports: Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid,
        reshape2, stats, utils, DOSE, clusterProfiler, pathview,
        enrichplot, msigdbr, depmap
Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap,
        png, scales, sva, BiocManager
NeedsCompilation: no
biocViews: FunctionalGenomics, CRISPR, PooledScreens, QualityControl,
        Normalization, GeneSetEnrichment, Pathways, Visualization,
        GeneTarget, KEGG
Encoding: UTF-8
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/MAGeCKFlute
git_branch: RELEASE_3_15
git_last_commit: 2a3e1ee
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
Packaged: 2022-04-26 23:21:50 UTC; biocbuild
Built: R 4.2.0; ; 2022-04-27 14:09:18 UTC; unix
