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Michael T. Wolfinger > Bio-ViennaNGS


This Release Bio-ViennaNGS-v0.18  [Download] [Browse 15 Feb 2018
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License The Perl 5 License (Artistic 1 & GPL 1)
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Bio::ViennaNGS A Perl distribution for Next-Generation Sequencing (NGS) data analysis     v0.18
Bio::ViennaNGS::AnnoC Object-oriented interface for storing and converting biological sequence annotation formats      
Bio::ViennaNGS::Bam High-level access to BAM files      
Bio::ViennaNGS::Bed Object-oriented interface for manipulation of genomic interval data in BED format      
Bio::ViennaNGS::Expression An object oriented interface for computing read-count based gene expression as TPM or RPKM      
Bio::ViennaNGS::ExtFeature A Moose wrapper for extended BED6-type genomic intervals.      
Bio::ViennaNGS::Fasta Moose wrapper for Bio::DB::Fasta      
Bio::ViennaNGS::Feature A Moose wrapper for BED6-type genomic intervals.      
Bio::ViennaNGS::FeatureChain Generic Moose wrapper class for combined/linked genomic intervals, eg BED12 elements      
Bio::ViennaNGS::FeatureIO Versatile I/O interface for Bio::ViennaNGS feature annotation classes      
Bio::ViennaNGS::FeatureInterval A Moose class for unstranded, elementary genomic intervals.      
Bio::ViennaNGS::MinimalFeature A Moose wrapper for stranded genomic intervals.      
Bio::ViennaNGS::Peak An object oriented interface for characterizing peaks in RNA-seq data      
Bio::ViennaNGS::SpliceJunc Perl extension for alternative splicing analysis      
Bio::ViennaNGS::Tutorial A collection of basic tutorials demonstrating of the core components and features of the Bio::ViennaNGS suite      
Bio::ViennaNGS::UCSC Perl extension for easy UCSC Genome Browser integration.      
Bio::ViennaNGS::Util Utility routines for Next-Generation Sequencing data analysis      

Documentation Construct a UCSC genome browser TrackHub Build UCSC genome browser Assembly Hubs from genomic sequence and annotation Split a BAM file by strands Make bigWig coverage profiles from BAM files Deconvolute BAM files into unique and multi mappers Convert BED or extended BED files to bedGraph format Get nucleotde and amino acid sequences from BED intervals Convert BED6 to BED12. Extract individual sequences from a multi Fasta file Find sequence motifs in a (multi) Fasta file Extract subsequence from a (multi) Fasta file Convert (non-spliced) GFF3 to BED12 Simple k-mer count analysis of fasta or fastq files Compute normalized expression data from read counts Identify peaks/enriched regions in RNA-seq data Produce BED12 from BED6 splice junction files. Find novel splice junctions in RNA-seq data. Build UCSC genome browser Track Hubs from genomic sequence and annotation Trim sequence and quality string of fastq files on the fly  

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