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.

Generated 2019-01-14 07:42:05 by Anduril 2.0.0