CRISPR AnalyzeR for Pooled CRISPR Screens


[Up] [Top]

Documentation for package ‘caRpools’ version 0.83

Help Pages

CRISPR-AnalyzeR-package CaRpools - CRISPR-AnalyzeR for pooled Screens
aggregatetogenes Aggregates pooled CRISPR screen sgRNA data to gene data
carpools.hit.overview Analysis: Analysis of pooled CRISPR screening data using a Wilcoxon Test
carpools.hit.scatter Plot: Plotting Scatters for hit candidate genes for all provided sampled
carpools.hit.sgrna Plotting sgRNA effects for all candidate genes or single genes
carpools.hitident Visualization of hit analysis performed by Wilcox, DESeq2 and MAGeCK
carpools.raw.genes Plotting sgRNA phenotype effects of a given gene
carpools.read.count.vs QC: Scatterplots of Read-Counts
carpools.read.depth QC: Plot Sequencing Read Depth
carpools.read.distribution QC: Plot Readcount Distribution
carpools.reads.genedesigns QC: Plot representation of sgRNAs per gene
carpools.sgrna.table Table Output of sgRNA effect and Target Sequence
carpools.waterfall.pval Visualization of p-value distribution
check.caRpools Test caRpools installation and dependent software
compare.analysis Exporting Hit Candidate Gene Information
CONTROL1 Read-count data for untreated sample, replicate 1
CONTROL1.g Read-count data for untreated sample, replicate 1
CONTROL2 Read-count data for untreated sample, replicate 2
CONTROL2.g Read-count data for untreated sample, replicate 2
CRISPR-AnalyzeR CaRpools - CRISPR-AnalyzeR for pooled Screens
d.CONTROL1 Name of Read-count data for untreated sample, replicate 1
d.CONTROL2 Name of Read-count data for untreated sample, replicate 2
d.TREAT1 Name of Read-count data for treated sample, replicate 1
d.TREAT2 Name of Read-count data for treated sample, replicate 2
data.extract Extracting sgRNA information from NGS FASTQ files to create read-count files for caRpools Analysis
final.table CaRpools: Generating Table with Analysis Information from all Methods
gene.remove Remove gene information from sgRNA data.frame
generate.hits Retrieving overlapping hits from caRpools analysis
get.gene.info Retrieving Gene Annotation and Gene Identifier Conversion from BiomaRt
libFILE FASTA file containing als sgRNA target sequences and identifiers. USed for mapping and sgRNA table.
load.file Load sgRNA NGS Data especially for caRpools
load.packages Loading and Installing packages used for caRpools
referencefile Name of fasta reference file without extension.
stat.DESeq Analysis: DESeq2 Analysis of pooled CRISPR NGS data
stat.mageck Analysis: Analysis of pooled CRISPR screening data using a MAGeCK
stat.wilcox Analysis: Analysis of pooled CRISPR screening data using a Wilcoxon Test
stats.data Calculating data set statistics
TREAT1 Read-count data for treated sample, replicate 1
TREAT1.g Read-count data for treated sample, replicate 1
TREAT2 Read-count data for treated sample, replicate 2
TREAT2.g Read-count data for treated sample, replicate 2
unmapped.genes sgRNAs without reads
use.caRpools Starting caRpools eport generation from R console