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Preprocessing

Description Imported data is filtered, normalized and checked against quality controls.
Child categories
Normalization ACGHnorm IlluminaNormalization LimmaNormalizer HTSeqExprNormalize LinearNormalizer AffyNormalization
Quality Control DuplicateQuality ExprMixtureModel SpatialContrast SpatialPlot ExtractCond BoxPlot MDSPlot
Filter GOFilter GOSearch MarkerCorrelations SequenceFilter CSVFilter QuantileFilter SampleCombiner TableQuery VariationFilter
Component Version Inputs Outputs Description
ACGHnorm 1.4 caseIn, control, admixtureMatrix, probeAnnotation casechannel, controlchannel, fit Normalizes two channel array CGH data with LOESS, median or mode.
AnnotateDrugs 1.0 in, annotations out Annotate drug concentrations.
CellGrowthAssay 1.0 in out, plots Compute the plate statistics for the plate survival assays and for dummy plates.
CombinationMatrix 1.0 in out, matrices, plots Compute the plate statistics for the plate survival assays and for dummy plates.
ControlsQCs 1.0 in out, plots Compute the plate statistics for the plate survival assays and for dummy plates.
CSVTransformer 1.1 csv1, csv2, columnNamesFile, array out Transforms CSV files using R expressions.
DSRTplots 1.0 in, annotations out, normalized, plots, combined, scores Plots the inhibition curves for each screening experiments, combine plots for different pretreatment times and computes the scores indicating the efficacy of each drug.
FastQScreen 1.0 dbList, reads, mates folder, NoHitPercentage FastQScreen allows you to screen a library of sequences in FastQ format against a set of sequence databases, for example vectors, virus or ribosomal RNA, so you can see if the composition of the library matches with what you expect.
FillNA 0.1 in out Fills NA values with linear interpolation or previous value.
FolderSplit 1.1 in out Divides files evenly from a folder in to N folders in an array.
MatrixRank 1.0 in out Computes ranks of values in a matrix.
MicroplateReader 1.0 in, annotations out Reads multiple XLSX files generated by a fluorescence/luminescence reader for a 96 or 384 well plate and converts it into a tab-delimitted CSV file with the correct annotations for each well.
PlateQCs 1.0 in out, plots Compute the plate statistics for the plate survival assays and for dummy plates.
SampleGroupCreator 1.2.2 data1, data2, data3 groups Creates sample group tables based on sample names read from data files.
SignificantCurves 1.0 in out, plots, auc Selects drugs based on their efficacy scores.
SmallRNAPrep 1.0 reads fastq, stats Uses FASTX-Toolkit to perform adapter trimming, artifact filtering, base-quality filtering, and read trimming for single-end read data.
SmallRNAQC 1.0 reads, mates, stats, bam, mergeStats qc, report, fastqc Performs all 3 quality filtering steps (preprocessing, alignment to genome, and optional alignment to transcripts) in the smallRNA pipelines.

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