Up: Components summary
Up: Components summary
Author
Lauri Lyly| Component | Version | Inputs | Outputs | Description |
|---|---|---|---|---|
| AnnTools | 0.1 | variants | array, log | Runs one of the AnnTools variant annotator suite's scripts. |
| CGHubDownload | 0.1 | key, analysisIds | queryResults, queryResultCSV, data | Executes CGHub's GeneTorrent package's utilities. |
| GroupFiles | 0.1 | in | out | Produces a CSV annotated by parsing path names containing named groups. |
| iSeq | 1.0 | treatment, control | peaks, report | Wraps the iSeq R package that implements the methods described in "A fully Bayesian hidden Ising model for ChIP-seq data analysis" by Qianxing Mo. |
| RankScore | 1.0 | inClasses, ranks, genes | scores, outClasses | Calculates a score matrix for a dichotomially classified set of samples. |
| RegionConvert | 0.1 | file, array, folder | file, array, folder | Converts files containing genomic or other sequence related regions to other formats retaining all applicable information. |
| RegionTransformer | 0.3 | regions, region_set, folder, scriptFile | result, array, folder | Computes DNA region set operations such as union and overlap. |
| ScriptIGV | 0.1 | scriptFile, file, array, tracks, session, igv | screenshots | Still under construction! Only the one file input and bedtools igv mode work at the moment, as evidenced by the only test case. |
| SISSRs | 1.0 | treatment, control, exclude | output | SISSRs is a software application for precise identification of genome-wide transcription factor binding sites from ChIP-Seq data. |
| SPP | 1.0 | treatment, control | peaks | Wraps the SPP R package from http://compbio.med.harvard.edu/Supplements/ChIP-seq/ published in Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. |
| STAR | 2.0 | genome, reads, mates, parameters | folder, alignment, spliceJunctions | Spliced Transcripts Alignment to a Reference for RNA-seq The reason to implement STAR component was that TopHat is around 50 times slower, and that time is counted in days. |
| STARGenome | 0.1 | genomeFasta, annotation, spliceJunctions | genome | Spliced Transcripts Alignment to a Reference for RNA-seq See the STAR component for more documentation. |
| Traph | 0.1 | fragments | folder | Traph RNA-seq abundance estimator from Veli Mäkinen lab. |
| VariantAnnotator | 0.4 | variantQuery, reference | calls, log, raw | This component is not being actively maintained currently, since Annovar is updated to frequently. |
| VCMM | 0.1 | pileup | indel, snp, summary | A variant caller, from VCMM website. |