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Description Tools that enable fetching annotations from external and internal databases.
Component Version Inputs Outputs Description
AffySNPFetch 1.0 markernames, connection rsnumbers Fetches SNP rs-numbers from Ensembl based on Affy SNP-ids.
AnnotEnsembl 1.0 annot Takes the ncRNA fasta file downloaded from Ensembl and creates a gff file with the transcript IDs as the reference chromosome.
AnnotMirbase 1.0 annot Takes a GFF3 file downloaded from miRBase and modifies the genomic locations to reference by Ensembl transcript ID (instead of chromosome) and relative positions inside the transcript ID (start and end positions).
Annovar 1.0 csvIn, vcfIn csvOut, vcfOut, analysis The component annotates genetic variants using ANNOVAR (table_annovar).
BiomartAnnotator 1.3 filter annotations, databases Fetches attributes with given filters using BioMart.
CreateSQLiteDB 0.1 DBlist Create miRNA-target gene database(s) for fast and simple SQLite query of potentially interesting regulatory pairs.
EnsemblChromosomes 1.0 connection chromosomes, extraChr Retrieves the Ensembl names and lengths of chromosomes.
EnsemblDNA 1.0 regions, connection sequences Fetches DNA sequences from the Ensembl database.
EnsemblGenes 1.0 connection codingGene, otherGene Retrieves the Ensembl gene locations.
EntrezAnnotator 1.0 in out Retrieves database records from NCBI Entrez, including gene annotation, PubMed references and sequences.
ExonAnnotator 1.0 query, dbConnect table Maps gene, transcript or exon Ensembl IDs to one another via the Ensembl query interface.
FusionAnalyzer 1.0 in, csvs out, folder Post-processing tool for gene fusion analysis.
GenomicVariantAnnotator 2.0 inputT table Queries the Database of Genomic Variants.
GOProbabilityTable 1.0 goAnnotation similarityTable, enrichmentTable Creates custom a priori probability tables for GO similarity and enrichment analysis.
GTFParser 1.0 in out Extracts field contents from a GTF file to output a CSV file.
IlluminaAnnotator 13.10 in out Fetches genomic annotations for Illumina methylation and expression array probes.
KorvasieniAnnotator 1.9 sourceKeys, connection bioAnnotation Converts gene, transcription, and translation identifiers using Korvasieni.
LocationVariation 1.0 locations, variationDatabase variations, populations Gets variation from Ensembl from a genomic location.
MotifMatch 1.7.1 motifs, sequence, seqSelection, bgIn, exclude hits, frequencies, bgOut Aligns the given motifs against the DNA sequencies.
NextGene 1.5.1 sourceKeys, connection bioAnnotation Finds the closest gene, exon, or transcript for the given loci.
PeakScore 1.2 in out Calculates a cumulative score for each gene having some regions assigned to it.
PINA 1.1 query interactions, network Finds the interacting proteins of query proteins for a list of query Uniprot ACs.
RangeMatch 1.0 positions, ranges result Component for 'left join' using keys and ranges.
RefSNPAnnotator 1.1.3 rsIDs annotations, geneChanges, databases Fetches annotations for given SNP rsID's with biomaRt.
RNAFold 1.0 sequence structure Predicts RNA secondary structure using Vienna RNA Package energy minimization function.
SNPs3DSearch 1.0 queryFeatures associatedGenes Fetches disease associated genes from the SNPs3D database.
TumorscapeReader 2.0 queryGenes, database features Connects to the Tumorscape database and outputs chromosomal aberration information for the query genes.

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