Tools

From gdroc:
- rave: RAVE (Rapid Allelic Variant Extractor) : Extract data from binary PLINK file
From iuc:
- featurecounts: Counts reads aligned to annotated genes in a reference genome from SAM or BAM files.
  - quast: Quast (Quality ASsessment Tool) evaluates genome assemblies by computing various metrics, including - N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length, - NG50, where length of the reference genome is being covered, - NA50 and NGA50, where aligned blocks instead of contigs are taken, - misassemblies, misassembled and unaligned contigs or contigs bases, - genes and operons covered.
  - scikit_bio_diversity_beta_diversity: Wrapper for the scikit-bio tool suite: Beta Diversity scikit-bio is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics
  - data_source_iris_tcga: Data source tool Retrieve data from Information Retrieval and Integration System for cancer genomic data from The Cancer Genome Atlas (IRIS-TCGA). IRIS-TCGA is an online web service for searching, retrieving and integrating genomic data: http://bioinf.iasi.cnr.it/iristcga/index.php.
  - bwameth: Fast and accurate alignment of BS-seq reads. Supports single-end and paired-end alignments and gapped alignments and is faster and more sensitive than many other tools
  - star_fusion: STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the intial STAR setup). https://github.com/STAR-Fusion/STAR-Fusion
From bgruening:
- deeptools_plot_enrichment: Wrapper for the deepTools: plotEnrichment. deepTools address the challenge of visualizing the large amounts of data that are now routinely generated from sequencing centers in a meaningful way. For a gallery of images that can be produced and a description of the tools see http://f1000.com/posters/browse/summary/1094053. https://github.com/fidelram/deepTools, doi: 10.1093/nar/gku365,
  - Wikipage: https://github.com/fidelram/deepTools/wiki
  - Repository-Maintainer: Björn Grüning, https://github.com/fidelram/deepTools
- nucleosome_prediction: Prediction of Nucleosomes Positions on the Genome. This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model
From saharlcc:
- isoem2_isode2: Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data
From amadeo:
- amadeo: This workflow can be applied to microarray data in order to find connections between genetic elements. This workflow extracts genetic information from this microarray data, and finds relationships between cis-regulatory elements located in the promoter under same regulation of gene expression.
From davidvanzessen:
- prisca: PRISCA: PRecISe Clonal Analysis Comparison of clonal sequences in paired samples

Dependency Definitions

From abretaud:
- package_lordec_0_6: Lordec 0.6 package