Search Results for "java modelling tools"

PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic...

This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function.

...Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk

cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.