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

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.

AuthorRussell Bainer, Dariusz Ratman, Pete Haverty, Steve Lianoglou
Date of publicationNone
MaintainerRussell Bainer <bainer.russell@gene.com>
LicenseArtistic-2.0
Version1.0.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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