Up: Components summary Author

Erkka Valo

Component Version Inputs Outputs Description
BiomartAnnotator 1.3 filter annotations, databases Fetches attributes with given filters using BioMart.
ClusterFiltering 1.0 fcsDir, in filtered, out Filters columns and/or rows from by clusters using flexible criteria.
EnsemblDNA 1.0 regions, connection sequences Fetches DNA sequences from the Ensembl database.
FlowMeans 1.0 inList, in clustersList, clusters, report Clusters rows in CSV files.
GOClustering 1.1.3 goAnnotations, expr, similarityTable report, clusters Clusters genes based on their gene ontology (GO) annotations.
MACS 1.1 treatment, control peaks, negativePeaks, report, wiggle, bedGraph Finds peaks from aligned short-reads.
MotifMatch 1.7.1 motifs, sequence, seqSelection, bgIn, exclude hits, frequencies, bgOut Aligns the given motifs against the DNA sequencies.
OptimalClustering 1.0 clusters, clustStat clusters, report The component takes the output of the MMClustering component, where each data sample has been clustered with multiple different cluster numbers, and determines the optimal cluster number for each sample.
PairWiseClusterPlot 1.0 clusterFiles, clusters, filteredFiles, filtered report Produces pairwise scatter plots from clustered and filtered data.
QCFasta 5.0 reads, mates, fastQCfolders, adapter qcReads, qcMates, report, table, qcUnpairedReads, qcUnpairedMates Quality control function for high-throughput sequencing data.
REvaluate 2.2 script, table1, table2, table3, table4, table5, var1, var2, var3, inArray table, outArray, optOut1, optOut2, optOut3, document Executes an R script that generates a matrix from the given data.
RNAFold 1.0 sequence structure Predicts RNA secondary structure using Vienna RNA Package energy minimization function.
Trimmomatic 2.1 read, mate, adapter trimmedReads, stdout, stats, log Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
VennDiagram 1.1.2 in report, out Draws Venn diagrams showing the intersections of the given sets of identifiers.

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