| 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. |
Up: Category summary
Annotation