| 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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Preprocessing