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.

Generated 2019-02-08 07:42:06 by Anduril 2.0.0