gCrisprTools-package |
gCrisprTools |
aln |
Precalculated alignment statistics of a crispr screen |
ann |
Annotation file for a mouse Crispr library |
ct.alignmentChart |
View a Barchart Summarizing Alignment Statistics for a Crispr Screen |
ct.applyAlpha |
Apply RRA 'alpha' cutoff to RRAalpha input |
ct.DirectionalTests |
Compute Directional P-values from eBayes Output |
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.gRNARankByReplicate |
Visualization of Ranked gRNA Abundances by Replicate |
ct.guideCDF |
View CDFs of the ranked gRNAs or Targets present in a crispr screen |
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 screen |
ct.makeRhoNull |
Make null distribution for RRAalpha tests |
ct.normalizeBySlope |
Normalize sample abundance estimates by the slope of the values in the a central range |
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 nontargeting control guides |
ct.normalizeSpline |
Normalize sample abundance estimates by a spline fit to the nontargeting controls |
ct.PantherPathwayEnrichment |
Run a (limited) Pathway Enrichment Analysis on the results of a Crispr experiment. |
ct.PRC |
Generate a Precision-Recall Curve from a CRISPR screen |
ct.prepareAnnotation |
Check and optionally subset an annotation file for use in a Crispr Screen |
ct.rawCountDensities |
Visualization of Raw gRNA Count Densities |
ct.resultCheck |
Determine whether a supplied object contains the results of a Pooled Screen |
ct.ROC |
Generate a Receiver-Operator Characteristic (ROC) Curve from a CRISPR screen |
ct.stackGuides |
View a stacked representation of the most variable targets or individual guides within an experiment, as a percentage of the total aligned reads |
ct.targetSetEnrichment |
Test Whether a Specified Target Set is Enriched Within a Pooled Screen |
ct.topTargets |
Display the log2 fold change estimates and associated standard deviations of the guides targeting the top candidates in a crispr screen |
ct.viewControls |
View nontargeting guides within an experiment |
ct.viewGuides |
Generate a Plot of individual gRNA Pair Data in a Crispr Screen |
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 |