View on
MetaCPAN
Michael T. Wolfinger > Bio-ViennaNGS

Bio-ViennaNGS

This Release Bio-ViennaNGS-v0.17.1  [Download] [Browse 10 Jun 2017
Other Releases
Links Discussion Forum ] [ View/Report Bugs ] [ Dependencies ] [ Other Tools ]
CPAN Testers PASS (2)   NA (28)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating      (0 Reviews) [ Rate this distribution ]
License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
AUTHORS
Changes
Makefile.PL
MANIFEST
META.json
README

Modules

Bio::ViennaNGS A Perl distribution for Next-Generation Sequencing (NGS) data analysis     v0.17.1
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::BedGraphEntry      
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::FeatureLine      
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::Subtypes      
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

Tutorial_Pipeline03.pl Construct a UCSC genome browser TrackHub  
assembly_hub_constructor.pl Build UCSC genome browser Assembly Hubs from genomic sequence and annotation  
bam_split.pl Split a BAM file by strands  
bam_to_bigWig.pl Make bigWig coverage profiles from BAM files  
bam_uniq.pl Deconvolute BAM files into unique and multi mappers  
bed2bedGraph.pl Convert BED or extended BED files to bedGraph format  
bed2nt2aa.pl Get nucleotde and amino acid sequences from BED intervals  
bed62bed12.pl Convert BED6 to BED12.  
fasta_multigrep.pl Extract individual sequences from a multi Fasta file  
fasta_subgrep.pl Extract subsequence from a (multi) Fasta file  
gff2bed.pl Convert (non-spliced) GFF3 to BED12  
kmer_analysis.pl Simple k-mer count analysis of fasta or fastq files  
normalize_multicov.pl Compute normalized expression data from read counts  
rnaseq_peakfinder.pl Identify peaks/enriched regions in RNA-seq data  
sj_visualizer.pl Produce BED12 from BED6 splice junction files.  
splice_site_summary.pl Find novel splice junctions in RNA-seq data.  
track_hub_constructor.pl Build UCSC genome browser Track Hubs from genomic sequence and annotation  
trim_fastq.pl Trim sequence and quality string of fastq files on the fly  

Other Files

share/template-AssemblyHub/description.html
share/template-TrackHub/description.html