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Short-read Sequencing

Parent category Analysis
Description Analysis of sequencing data produced by next-generation sequencing platforms e.g. Illumina/Solexa
Component Version Inputs Outputs Description
DESeqExpr 1.0 geneCounts, sampleNames expr, log2 Provides a gene expression matrix using DESeq.
FusionMap 1.0 reads, mates fusions, fusionReads Detect genomic fusions from paired or single ended DNA-seq or RNA-seq data using FusionMap.
GenomicRearrangement 0.1 reference, input, folder delly Call genomic rearrangments.
MACS 1.1 treatment, control peaks, negativePeaks, report, wiggle, bedGraph Finds peaks from aligned short-reads.
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.
RegionOverlap 1.2 regions1, regions2 regions Produces a list of overlapping DNA regions.
RegionReport 1.1 regions, chromosomes report Generates statistics about the DNA regions.
SPINLONG 1.0 bedFiles, patterns, regions, chromosomes, mappability, control scores, plots, patternsDump Identify user-defined spatio-temporal patterns in ChIP-seq and other sequencing data using the SPINLONG method.

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