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Bio-ViennaNGS-v0.19.2
River stage zero No dependents
2 ++

Changes for version 0.19.2

  • added FeatureBase role; adjusted Feature classes & tests

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_regex.pl
Find sequence motifs in 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

Modules

Bio::ViennaNGS
A Perl distribution for Next-Generation Sequencing (NGS) data analysis
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::FeatureBase
A Moose Role for BED compliance
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::FeatureIntervalN
A Moose wrapper for named 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

Other files