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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