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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gCrisprTools")
AuthorRussell Bainer, Dariusz Ratman, Pete Haverty, Steve Lianoglou
Bioconductor views BiomedicalInformatics CRISPR CellBiology DifferentialExpression ExperimentalDesign FunctionalGenomics GeneSetEnrichment Genetics MultipleComparison Normalization Pharmacogenetics Pharmacogenomics PooledScreens Preprocessing QualityControl RNASeq Regression Software SystemsBiology Visualization
Date of publicationNone
MaintainerRussell Bainer <haverty.peter@gene.com>
LicenseArtistic-2.0
Version1.4.0

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.applyAlpha: Apply RRA 'alpha' cutoff to RRAalpha input

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.makeRhoNull: Make null distribution for RRAalpha tests

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

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

Functions

aln Man page
ann Man page
appendDateAndExt Man page
ct.alignmentChart Man page
ct.alphaBeta Man page
ct.applyAlpha Man page
ct.DirectionalTests Man page
ct.drawColorLegend Man page
ct.drawFlat Man page
ct.ecdf Man page
ct.exprsColor Man page
ct.filterReads Man page
ct.GCbias Man page
ct.generateResults Man page
ct.getPanther Man page
ct.gRNARankByReplicate Man page
ct.guideCDF Man page
ct.inputCheck Man page
ct.makeContrastReport Man page
ct.makeQCReport Man page
ct.makeReport Man page
ct.makeRhoNull Man page
ct.normalizeBySlope Man page
ct.normalizeGuides Man page
ct.normalizeMedians Man page
ct.normalizeNTC Man page
ct.normalizeSpline Man page
ct.numcores Man page
ct.PantherPathwayEnrichment Man page
ct.PRC Man page
ct.prepareAnnotation Man page
ct.preprocessFit Man page
ct.rawCountDensities Man page
ct.resultCheck Man page
ct.ROC Man page
ct.RRAalpha Man page
ct.RRAalphaBatch Man page
ct.RRAaPvals Man page
ct.stackGuides Man page
ct.targetSetEnrichment Man page
ct.topTargets Man page
ct.viewControls Man page
ct.viewGuides Man page
dir.writable Man page
es Man page
essential.genes Man page
fit Man page
gCrisprTools-package Man page
initOutDir Man page
renderReport Man page
resultsDF Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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