Documentation
Generates a simple statistic with ggplots about the sequence coverage of motifs from MEME standard xml output
Inferring quantitative and qualitative parameters from an input BAM file.
An example pipeline for the ViennaNGS toolbox
Another example pipeline for the ViennaNGS toolbox
Construct a UCSC genome browser trackhub
Build UCSC genome browser Assembly Hubs from genomic sequence and annotation
Generates quality statistics from specified BAM input files.
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
Extends bed entries strand specific one- or two-sided.
Convert (non-spliced) GFF3 to BED12
Simple k-mer count analysis of fasta or fastq files
Compute normalized expression data from read counts
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
Trims sequence and quality string of fastq files on the fly
Modules
A Perl distribution for Next-Generation Sequencing (NGS) data analysis
Object-oriented interface for storing and converting biological sequence annotation formats
High-level access to BAM files
Moose interface to BAM mapping statistics
Moose interface for analyzing, summarizing and comparing BAM mapping statistics produced by Bio::ViennaNGS::BamStat
Object-oriented interface for manipulation of genomic interval data in BED format
An object oriented interface for computing read-count based gene expression as TPm or RPKM
Moose wrapper for Bio::DB::Fasta
Perl extension for alternative splicing analysis
A collection of basic tutorials demonstrating of the core components and features of the Bio::ViennaNGS suite
Perl extension for easy UCSC Genome Browser integration.
Utility routines for Next-Generation Sequencing data analysis
Provides
in lib/Bio/ViennaNGS/ExtFeature.pm
in lib/Bio/ViennaNGS/Feature.pm
in lib/Bio/ViennaNGS/FeatureChain.pm
in lib/Bio/ViennaNGS/FeatureLine.pm
in lib/Bio/ViennaNGS/MinimalFeature.pm