Up: Components summary Author

Ping Chen

Component Version Inputs Outputs Description
AffyReader 1.1.2 affy, sampleNames expr, exprRaw, groups Imports gene expression or exon array data from Affymetrix CEL-files.
AlignStats 1.2 alignment, reference, annotation, refgene, chromsize, log report, stats Evaluate sequencing data, especially RNA-seq data quality using RSeQC.
AutoGating 1.0 rule, clusters, array filtered, filteredArray, population, populationArray Automatically gate cell populations.
Blast 1.0 query, dbSeq result Basic local alignment search tool.
ClusterChooser 1.0 population, plots, sampleAnnotation corrected, fileStatus Graphical tool for cluster population selection.
ClusterFiltering 1.0 fcsDir, in filtered, out Filters columns and/or rows from by clusters using flexible criteria.
DEE2DEG 1.0 dee, dbConnect deg Find differentially expressed genes (DEG) based on differentially expressed exons (DEE).
EnsemblDNA 1.0 regions, connection sequences Fetches DNA sequences from the Ensembl database.
EnsemblGenes 1.0 connection codingGene, otherGene Retrieves the Ensembl gene locations.
ExonAnnotator 1.0 query, dbConnect table Maps gene, transcript or exon Ensembl IDs to one another via the Ensembl query interface.
ExonExpression 1.0 expr, sample, exon ExonExpr Converts exon expression matrix for a list of exons of interest.
ExonToPeptide 1.0 ExonList, connection ExonSeq, PeptideSeq Fetches exon-peptide sequences of query exon list.
FASTA2CSV 1.0 in out Converts a FASTA file to CSV.
FastQC 2.0 read, mate summary, report, extra, folder Short reads quality control for high-throughput sequencing data.
GatingSummary 1.0 summaries, sampleAnnotation, panel, population summaryResult, report Generate summay report table and heatmap.
GetUtrSeq 1.0 transcripts, connection UTR5, UTR3 Fetch UTR sequences of query transcripts.
GlobalCorrelation 1.2 gene, mirna correlated_filtered, correlated_all, expression_miRNA, expression_mRNA Compute correlation between miRNA and gene/transcript expression.
GOClustering 1.1.3 goAnnotations, expr, similarityTable report, clusters Clusters genes based on their gene ontology (GO) annotations.
LimmaStat 1.0 expr, sampleAnnotation sigTarget Select differentially expressed probesets, exons or transcripts from probeset, exon or transcript expression data by using limma statistical test.
MeapNormalization 2.0 affy, sampleNames normalized Prepares normalized data at probe level.
MeapQuantification 2.0 normalized, dbConnect ExonExpr, SpliceVariantExpr, GeneExpr Quantify expression data on exon, splicing variant or gene level.
MeapVisualizer 1.0 expr, geneList, dbConnect, sample report Generate visualization for genes of interest with spliced isoforms.
MirMatch 1.0 utrSeeds, matureSeq, pairs matched String match for between mature miRNA seeds and target UTR seeds.
QCParser 1.0 summary basicStats, perBaseSeqQual, perSeqQualScore, perBaseSeqContent, perBaseGC, perSeqGC, perBaseN, seqDuplicateLevel, overrepresented Parse SeqQC summary result.
Trimmer 1.0 data, perBaseSeqQual, trimInfo trimmedReads Trim sequence reads at both ends.
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.
UtrSeq2Seeds 1.0 utrseq seeds Generate seeds with 15bp (XXXXXXXQXXXXXXX) with each query loci in middle.

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