gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

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Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting.

Author
Russell Bainer, Dariusz Ratman, Pete Haverty, Steve Lianoglou
Date of publication
None
Maintainer
Russell Bainer <bainer.russell@gene.com>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

aln
Precalculated alignment statistics of a crispr screen
ann
Annotation file for a mouse Crispr library
appendDateAndExt
Add formatted timestamp and extension to a file name
ct.alignmentChart
View a Barchart Summarizing Alignment Statistics for a Crispr...
ct.alphaBeta
Aggregation of P-value Ranks using a Beta Distribution and...
ct.DirectionalTests
Compute Directional P-values from eBayes Output
ct.drawColorLegend
Draw a density color legend.
ct.drawFlat
Draw a horizontal line of a specified color.
ct.ecdf
Generate a cumulative tally of reads by guide rank
ct.exprsColor
Assign Colors Based on the Position of a Value in a...
ct.filterReads
Remove low-abundance elements from an ExpressionSet object
ct.GCbias
Visualization of gRNA GC Content Trends
ct.generateResults
Calculate results of a crispr screen from a contrast
ct.getPanther
Extract a Named List of Entrez IDs Annotated to Each Pathway...
ct.gRNARankByReplicate
Visualization of Ranked gRNA Abundances by Replicate
ct.guideCDF
View CDFs of the ranked gRNAs or Targets present in a crispr...
ct.inputCheck
Check compatibility of a sample key with a supplied object
ct.makeContrastReport
Generate a Contrast report from a pooled CRISPR screen
ct.makeQCReport
Generate a QC report from a pooled CRISPR screen
ct.makeReport
Generate a full experimental report from a pooled CRISPR...
ct.normalizeBySlope
Normalize sample abundance estimates by the slope of the...
ct.normalizeGuides
Normalize an ExpressionSet Containing a Crispr Screen
ct.normalizeMedians
Normalize sample abundance estimates by median gRNA counts
ct.normalizeNTC
Normalize sample abundance estimates by the median values of...
ct.normalizeSpline
Normalize sample abundance estimates by a spline fit to the...
ct.numcores
Checks and Possibly Sets the Number of Cores to be Used in...
ct.PantherPathwayEnrichment
Run a (limited) Pathway Enrichment Analysis on the results of...
ct.PRC
Generate a Precision-Recall Curve from a CRISPR screen
ct.prepareAnnotation
Check and optionally subset an annotation file for use in a...
ct.preprocessFit
Preprocess a "MArrayLM" model fit object to include only one...
ct.rawCountDensities
Visualization of Raw gRNA Count Densities
ct.resultCheck
Determine whether a supplied object contains the results of a...
ct.ROC
Generate a Receiver-Operator Characteristic (ROC) Curve from...
ct.RRAalpha
Aggregation of P-value Ranks using a Beta Distribution and...
ct.RRAalphaBatch
Create Batches of Null Permutations for a Crispr Screen
ct.RRAaPvals
gRNA signal aggregation via RRAa, optionally using multiple...
ct.stackGuides
View a stacked representation of the most variable targets or...
ct.targetSetEnrichment
Test Whether a Specified Target Set is Enriched Within a...
ct.topTargets
Display the log2 fold change estimates and associated...
ct.viewControls
View nontargeting guides within an experiment
ct.viewGuides
Generate a Plot of individual gRNA Pair Data in a Crispr...
dir.writable
Checks that the directory provided is writable by the current...
es
ExpressionSet of count data from a Crispr screen with strong...
essential.genes
Artificial list of 'essential' genes in the example Crispr...
fit
Precalculated contrast fit from a Crispr screen
gCrisprTools-package
gCrisprTools
initOutDir
Initializes the output directory
renderReport
Internal wrapper to generate html markdown reports from...
resultsDF
Precalculated gene-level summary of a crispr screen

Files in this package

gCrisprTools/DESCRIPTION
gCrisprTools/NAMESPACE
gCrisprTools/NEWS
gCrisprTools/R
gCrisprTools/R/AlignmentBarchart.R
gCrisprTools/R/Crispr_Enrichment_test.R
gCrisprTools/R/DirTest.R
gCrisprTools/R/ExtractKeyFromAnnotation.R
gCrisprTools/R/GCbias.R
gCrisprTools/R/GenePvalsFromEset.R
gCrisprTools/R/GeneratePRC.R
gCrisprTools/R/GenerateROC.R
gCrisprTools/R/GuideCDF.R
gCrisprTools/R/NormalizeByNTCLoess.R
gCrisprTools/R/NormalizeBySlope.R
gCrisprTools/R/RRAalpha.R
gCrisprTools/R/RankByRep.R
gCrisprTools/R/Raw_read_densities.R
gCrisprTools/R/StackedGuides.R
gCrisprTools/R/ViewControls.R
gCrisprTools/R/ViewGuides.R
gCrisprTools/R/ViewTopTargets.R
gCrisprTools/R/discardTraceReads.R
gCrisprTools/R/fileutilities.R
gCrisprTools/R/gCrisprTools.R
gCrisprTools/R/generateReports.R
gCrisprTools/R/processFit.R
gCrisprTools/build
gCrisprTools/build/vignette.rds
gCrisprTools/data
gCrisprTools/data/aln.RData
gCrisprTools/data/ann.RData
gCrisprTools/data/datalist
gCrisprTools/data/es.RData
gCrisprTools/data/essential.genes.RData
gCrisprTools/data/fit.RData
gCrisprTools/data/resultsDF.RData
gCrisprTools/inst
gCrisprTools/inst/Mageck_&_gCrisprTools.html
gCrisprTools/inst/doc
gCrisprTools/inst/doc/Crispr_example_workflow.R
gCrisprTools/inst/doc/Crispr_example_workflow.Rmd
gCrisprTools/inst/doc/Crispr_example_workflow.html
gCrisprTools/inst/doc/gCrisprTools_Vignette.R
gCrisprTools/inst/doc/gCrisprTools_Vignette.Rmd
gCrisprTools/inst/doc/gCrisprTools_Vignette.html
gCrisprTools/inst/gCrisprTools_package_design.pptx
gCrisprTools/inst/rmarkdown
gCrisprTools/inst/rmarkdown/templates
gCrisprTools/inst/rmarkdown/templates/CRISPR_QC_report
gCrisprTools/inst/rmarkdown/templates/CRISPR_QC_report/skeleton
gCrisprTools/inst/rmarkdown/templates/CRISPR_QC_report/skeleton/skeleton.Rmd
gCrisprTools/inst/rmarkdown/templates/CRISPR_QC_report/template.yaml
gCrisprTools/inst/rmarkdown/templates/CRISPR_contrast_report
gCrisprTools/inst/rmarkdown/templates/CRISPR_contrast_report/skeleton
gCrisprTools/inst/rmarkdown/templates/CRISPR_contrast_report/skeleton/skeleton.Rmd
gCrisprTools/inst/rmarkdown/templates/CRISPR_contrast_report/template.yaml
gCrisprTools/inst/rmarkdown/templates/CRISPR_report
gCrisprTools/inst/rmarkdown/templates/CRISPR_report/skeleton
gCrisprTools/inst/rmarkdown/templates/CRISPR_report/skeleton/skeleton.Rmd
gCrisprTools/inst/rmarkdown/templates/CRISPR_report/template.yaml
gCrisprTools/man
gCrisprTools/man/aln.Rd
gCrisprTools/man/ann.Rd
gCrisprTools/man/appendDateAndExt.Rd
gCrisprTools/man/ct.DirectionalTests.Rd
gCrisprTools/man/ct.GCbias.Rd
gCrisprTools/man/ct.PRC.Rd
gCrisprTools/man/ct.PantherPathwayEnrichment.Rd
gCrisprTools/man/ct.ROC.Rd
gCrisprTools/man/ct.RRAaPvals.Rd
gCrisprTools/man/ct.RRAalpha.Rd
gCrisprTools/man/ct.RRAalphaBatch.Rd
gCrisprTools/man/ct.alignmentChart.Rd
gCrisprTools/man/ct.alphaBeta.Rd
gCrisprTools/man/ct.drawColorLegend.Rd
gCrisprTools/man/ct.drawFlat.Rd
gCrisprTools/man/ct.ecdf.Rd
gCrisprTools/man/ct.exprsColor.Rd
gCrisprTools/man/ct.filterReads.Rd
gCrisprTools/man/ct.gRNARankByReplicate.Rd
gCrisprTools/man/ct.generateResults.Rd
gCrisprTools/man/ct.getPanther.Rd
gCrisprTools/man/ct.guideCDF.Rd
gCrisprTools/man/ct.inputCheck.Rd
gCrisprTools/man/ct.makeContrastReport.Rd
gCrisprTools/man/ct.makeQCReport.Rd
gCrisprTools/man/ct.makeReport.Rd
gCrisprTools/man/ct.normalizeBySlope.Rd
gCrisprTools/man/ct.normalizeGuides.Rd
gCrisprTools/man/ct.normalizeMedians.Rd
gCrisprTools/man/ct.normalizeNTC.Rd
gCrisprTools/man/ct.normalizeSpline.Rd
gCrisprTools/man/ct.numcores.Rd
gCrisprTools/man/ct.prepareAnnotation.Rd
gCrisprTools/man/ct.preprocessFit.Rd
gCrisprTools/man/ct.rawCountDensities.Rd
gCrisprTools/man/ct.resultCheck.Rd
gCrisprTools/man/ct.stackGuides.Rd
gCrisprTools/man/ct.targetSetEnrichment.Rd
gCrisprTools/man/ct.topTargets.Rd
gCrisprTools/man/ct.viewControls.Rd
gCrisprTools/man/ct.viewGuides.Rd
gCrisprTools/man/dir.writable.Rd
gCrisprTools/man/es.Rd
gCrisprTools/man/essential.genes.Rd
gCrisprTools/man/fit.Rd
gCrisprTools/man/gCrisprTools-package.Rd
gCrisprTools/man/initOutDir.Rd
gCrisprTools/man/renderReport.Rd
gCrisprTools/man/resultsDF.Rd
gCrisprTools/vignettes
gCrisprTools/vignettes/Crispr_example_workflow.Rmd
gCrisprTools/vignettes/gCrisprTools_Vignette.Rmd