Package: QuasR 1.53.0

Introduction | Preliminaries | Citing r Biocpkg("QuasR") | Installation | Loading of QuasR and other required packages | How to get help | Quick Start | A brief introduction to R | Sample QuasR session | QuasR Overview | File storage locations | Example tasks | Create a sample file | Working only with bam files after performing alignments | Consistency of samples within a project | Create an auxiliary file (optional) | Select the reference genome | Choosing a suitable (non-redundant) reference genome | Sequence data pre-processing | Example workflows | ChIP-seq: Measuring protein-DNA binding and chromatin modifications | Align reads using the qAlign function | Create a quality control report | Alignment statistics | Export genome wig file from alignments | Count alignments using qCount | Create a genomic profile for a set of regions using qProfile | Using a r Biocpkg("BSgenome") package as reference genome | RNA-seq: Gene expression profiling | Spliced alignment of RNA-seq reads | Quantification of gene and exon expression | Calculation of RPKM expression values | Analysis of alternative splicing: Quantification of exon-exon junctions | smRNA-seq: small RNA and miRNA expression profiling | Preprocessing of small RNA (miRNA) reads | Alignment of small RNA (miRNA) reads | Quantification of small RNA (miRNA) reads | Bis-seq: Measuring DNA methylation | Allele-specific analysis | Description of Individual QuasR Functions | preprocessReads | qAlign | qProject class | qQCReport | alignmentStats | qExportWig | qCount | Determination of overlap | Running modes of qCount | qProfile | qMeth | Session information | References