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11 Dec 2018 13:25:00 UTC
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Bus factor: 0- License: perl_5
- Perl: v5.10.0
24 month- Download (1.21MB)
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Changes for version 0.19.2
- added FeatureBase role; adjusted Feature classes & tests
Documentation
Construct a UCSC genome browser TrackHubBuild UCSC genome browser Assembly Hubs from genomic sequence and annotationSplit a BAM file by strandsMake bigWig coverage profiles from BAM filesDeconvolute BAM files into unique and multi mappersConvert BED or extended BED files to bedGraph formatGet nucleotde and amino acid sequences from BED intervalsConvert BED6 to BED12.Extract individual sequences from a multi Fasta fileFind sequence motifs in a (multi) Fasta fileExtract subsequence from a (multi) Fasta fileConvert (non-spliced) GFF3 to BED12Simple k-mer count analysis of fasta or fastq filesCompute normalized expression data from read countsIdentify peaks/enriched regions in RNA-seq dataProduce BED12 from BED6 splice junction files.Find novel splice junctions in RNA-seq data.Build UCSC genome browser Track Hubs from genomic sequence and annotationTrim sequence and quality string of fastq files on the flyModules
A Perl distribution for Next-Generation Sequencing (NGS) data analysisObject-oriented interface for storing and converting biological sequence annotation formatsHigh-level access to BAM filesObject-oriented interface for manipulation of genomic interval data in BED formatAn object oriented interface for computing read-count based gene expression as TPM or RPKMA Moose wrapper for extended BED6-type genomic intervals.Moose wrapper for Bio::DB::FastaA Moose wrapper for BED6-type genomic intervals.A Moose Role for BED complianceGeneric Moose wrapper class for combined/linked genomic intervals, eg BED12 elementsVersatile I/O interface for Bio::ViennaNGS feature annotation classesA Moose class for unstranded, elementary genomic intervals.A Moose wrapper for named genomic intervals.A Moose wrapper for stranded genomic intervals.An object oriented interface for characterizing peaks in RNA-seq dataPerl extension for alternative splicing analysisA collection of basic tutorials demonstrating of the core components and features of the Bio::ViennaNGS suitePerl extension for easy UCSC Genome Browser integration.Utility routines for Next-Generation Sequencing data analysis
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