Package: gCrisprTools 2.13.0

Russell Bainer

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. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.

Authors:Russell Bainer, Dariusz Ratman, Steve Lianoglou, Peter Haverty

gCrisprTools_2.13.0.tar.gz
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gCrisprTools.pdf |gCrisprTools.html✨
gCrisprTools/json (API)
NEWS

# Install 'gCrisprTools' in R:
install.packages('gCrisprTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • aln - Precalculated alignment statistics of a crispr screen
  • ann - Annotation file for a mouse Crispr library
  • es - ExpressionSet of count data from a Crispr screen with strong selection
  • essential.genes - Artificial list of 'essential' genes in the example Crispr screen included for plotting purposes
  • fit - Precalculated contrast fit from a Crispr screen
  • resultsDF - Precalculated gene-level summary of a crispr screen

On BioConductor:gCrisprTools-2.13.0(bioc 3.21)gCrisprTools-2.12.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologycrisprpooledscreensexperimentaldesignbiomedicalinformaticscellbiologyfunctionalgenomicspharmacogenomicspharmacogeneticssystemsbiologydifferentialexpressiongenesetenrichmentgeneticsmultiplecomparisonnormalizationpreprocessingqualitycontrolrnaseqregressionsoftwarevisualization

4.78 score 8 scripts 202 downloads 2 mentions 49 exports 89 dependencies

Last updated 2 months agofrom:1bb7f87a1e. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:ct.alignmentChartct.alphaBetact.applyAlphact.buildSEct.CATct.compareContrastsct.contrastBarchartct.DirectionalTestsct.expandAnnotationct.filterReadsct.GCbiasct.generateResultsct.GREATdbct.gRNARankByReplicatect.guideCDFct.keyCheckct.makeContrastReportct.makeQCReportct.makeReportct.makeRhoNullct.normalizeBySlopect.normalizeFQct.normalizeGuidesct.normalizeMediansct.normalizeNTCct.normalizeSplinect.parseGeneSymbolct.PRCct.prepareAnnotationct.preprocessFitct.rankSimplect.rawCountDensitiesct.regularizeContrastsct.resultCheckct.ROCct.RRAalphact.RRAaPvalsct.scatterct.seasct.seasPrepct.signalSummaryct.simpleResultct.softLogct.stackGuidesct.targetSetEnrichmentct.topTargetsct.upSetct.viewControlsct.viewGuides

Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcrayoncurlDelayedArraydigestdoParallelevaluatefansifarverfastmapfontawesomeforeachfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehighrhtmltoolshttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigpngR6rappdirsRColorBrewerrjsonrlangrmarkdownRobustRankAggregS4ArraysS4VectorssassscalesshapeSparseArraystatmodSummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

Advanced Screen Analysis: Contrast Comparisons

Russell Bainer

Rendered fromContrast_Comparisons.Rmdusingknitr::knitron Nov 29 2024.

Last update: 2022-03-24
Started: 2021-03-16

Example Workflow For Processing a Single Pooled Screen

Russell Bainer

Rendered fromCrispr_example_workflow.Rmdusingknitr::knitron Nov 29 2024.

Last update: 2022-03-24
Started: 2016-09-12

gCrisprTools and the Analysis of Pooled Screening Data

Russell Bainer

Rendered fromgCrisprTools_Vignette.Rmdusingknitr::knitron Nov 29 2024.

Last update: 2021-10-01
Started: 2016-09-12

Readme and manuals

Help Manual

Help pageTopics
gCrisprToolsgCrisprTools-package
Precalculated alignment statistics of a crispr screenaln
Annotation file for a mouse Crispr libraryann
View a Barchart Summarizing Alignment Statistics for a Crispr Screenct.alignmentChart
Apply RRA 'alpha' cutoff to RRAalpha inputct.applyAlpha
Package Screen Data into a `SummarizedExperiment` Objectct.buildSE
Compare Two CRISPR Screens via a CAT plotct.CAT
Identify Replicated Signals in Pooled Screens Using Conditional Scoringct.compareContrasts
Visualize Signal Across A List of Contrastsct.contrastBarchart
Compute Directional P-values from eBayes Outputct.DirectionalTests
Expand an annotation object to allow annotations of reagents to multiple targetsct.expandAnnotation
Remove low-abundance elements from an ExpressionSet objectct.filterReads
Visualization of gRNA GC Content Trendsct.GCbias
Calculate results of a crispr screen from a contrastct.generateResults
Update a gene-centric msdb object for GREAT-style enrichment analysis using a specified CRISPR annotation.ct.GREATdb
Visualization of Ranked gRNA Abundances by Replicatect.gRNARankByReplicate
View CDFs of the ranked gRNAs or Targets present in a crispr screenct.guideCDF
Check compatibility of a sample key with a supplied objectct.inputCheck
Check compatibility of a sample key with a supplied ExpressionSet or similar objectct.keyCheck
Generate a Contrast report from a pooled CRISPR screenct.makeContrastReport
Generate a QC report from a pooled CRISPR screenct.makeQCReport
Generate a full experimental report from a pooled CRISPR screenct.makeReport
Make null distribution for RRAalpha testsct.makeRhoNull
Normalize sample abundance estimates by the slope of the values in the central rangect.normalizeBySlope
Apply Factored Quantile Normalization to an esetct.normalizeFQ
Normalize an ExpressionSet Containing a Crispr Screenct.normalizeGuides
Normalize sample abundance estimates by median gRNA countsct.normalizeMedians
Normalize sample abundance estimates by the median values of nontargeting control guidesct.normalizeNTC
Normalize sample abundance estimates by a spline fit to specific shared elementsct.normalizeSpline
Parse `geneSymbol` values to construct an alternative annotation listct.parseGeneSymbol
Generate a Precision-Recall Curve from a CRISPR screenct.PRC
Check and optionally subset an annotation file for use in a Crispr Screenct.prepareAnnotation
Rank Signals in a Simplified Pooled Screen Result Objectct.rankSimple
Visualization of Raw gRNA Count Densitiesct.rawCountDensities
Regularize Two Screening Results Objectsct.regularizeContrasts
Determine whether a supplied object contains the results of a Pooled Screenct.resultCheck
Generate a Receiver-Operator Characteristic (ROC) Curve from a CRISPR screenct.ROC
Compare Two CRISPR Screen Contrasts via a Scatter Plotct.scatter
Geneset Enrichment within a CRISPR screen using `sparrow`ct.seas
Prepare one or more resultsDF objects for analysis via Sparrow.ct.seasPrep
Generate a Figure Summarizing Overall Signal for One or More Targetsct.signalSummary
Convert a verbose results DF object to a gene-level result objectct.simpleResult
Log10 transform empirical P-values with a pseudocountct.softLog
View a stacked representation of the most variable targets or individual guides within an experiment, as a percentage of the total aligned readsct.stackGuides
Display the log2 fold change estimates and associated standard deviations of the guides targeting the top candidates in a crispr screenct.topTargets
Consolidate shared signals across many contrasts in an UpSet Plotct.upSet
View nontargeting guides within an experimentct.viewControls
Generate a Plot of individual gRNA Pair Data in a Crispr Screenct.viewGuides
ExpressionSet of count data from a Crispr screen with strong selectiones
Artificial list of 'essential' genes in the example Crispr screen included for plotting purposesessential.genes
Precalculated contrast fit from a Crispr screenfit
Precalculated gene-level summary of a crispr screenresultsDF