Simplified Results Objects | Testing Overlaps Between Two or More Screens | Visualization of Screen Enrichment and Depletion Dynamics | More Comparisons | Ontological Enrichment

1.0 Overview of gCrisprTools | 1.1 Installation | 1.4 Explore the Vignettes Folder | 1.3 Dependencies | 2.0 Inputs | 2.1 Counting Cassettes from Sequencing Data | 2.2 An ExpressionSet of Cassette Counts | 2.3 An Annotation Object | 2.4 A Sample Key | 2.5 Alignment Statistics | 3.0 Preprocess Raw Data | 3.1 ct.filterReads | 3.2 ct.normalizeGuides | 3.3 ct.makeQCReport | 4.0 Quality Assessment | 4.1 ct.rawCountDensities | 4.2 ct.gRNARankByReplicate | 4.3 ct.viewControls | 4.4 ct.guideCDF | 5.0 Identifying Candidate Targets | 5.1 ct.generateResults | 6.0 Visualization of Results | 6.1 ct.topTargets | 6.2 ct.stackGuides | 6.3 ct.viewGuides | 6.3 ct.signalSummary | 6.4 ct.makeContrastReport and ct.makeReport | 7.0 Hypothesis Testing | 7.1 ct.seas | 7.2 ct.targetSetEnrichment, ct.signalSummary, ct.ROC, and ct.PRC

Example Workflow For Processing a Single Screen | Alternative Annotations | Quality Control | Target-Level Visualization and Analysis