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DNA

Analyze transcription factors in ChIP-Seq and methylation data; detect statistically significant peaks or regions in coverage signal

Apps

NGS Browser Visualize and explore short-read sequence alignments

Functions

ngsbrowser Open NGS Browser to visualize and explore short-read sequence alignments
mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
mle Maximum likelihood estimates
nbinpdf Negative binomial probability density function
chromosomeplot Plot chromosome ideogram with G-banding pattern
cpgisland Locate CpG islands in DNA sequence
mspeaks Convert raw peak data to peak list (centroided data)
align2cigar Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format
cigar2align Convert unaligned sequences to aligned sequences using Compact Idiosyncratic Gapped Alignment Report (CIGAR) format
bowtie Map short reads to reference sequence using Burrows-Wheeler transform
bowtiebuild Generate index using Burrows-Wheeler transform

Classes

BioRead Contain sequence and quality data
BioMap Contain sequence, quality, alignment, and mapping data
BioReadQualityStatistics Quality statistics from a short-read sequence file
GFFAnnotation Represent General Feature Format (GFF) annotations
GTFAnnotation Represent Gene Transfer Format (GTF) annotations

Topics

Manage Short-Read Sequence Data in Objects

Use objects to store, manipulate, and retrieve short-read sequence data

Store and Manage Feature Annotations in Objects

Use feature annotation objects to investigate and filter sequence data

Visualize and Investigate Short-Read Alignments

Use NGS Browser to visualize and investigate short-read alignments and feature annotations against a single reference sequence

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