Introduction | Generate feature ranges | Extract feature sequences | Generate an expanded GTF file | Generate a transcript-to-gene mapping | Session info

Introduction | Installation | Preparing the annotation | Quantify RNA-seq alignments in exons and introns | Align reads | Count alignments in exons and gene bodies | Load full count tables | Run EISA conveniently | Alternative implementations of EISA | On the estimation of interactions in a split-plot design experiment | Visualize EISA results | Run EISA step-by-step | Normalization | Identify quantifiable genes | Calculate $\Delta I$, $\Delta E$ and $\Delta E - \Delta I$ | Statistical analysis | Visualize the results | Session information | References

Introduction | Installation | Quick example: Identify enriched motifs in bins | Binned motif enrichment analysis with multiple sets of sequences (more than two): Finding TFs enriched in differentially methylated regions | Load packages | Genomic regions or sequences of interest | Bin genomic regions | Prepare motif enrichment analysis | Run motif enrichment analysis | Convert between motif text file for Homer and motif objects in R | Motif enrichment analysis with only one or two sets of sequences | Binary motif enrichment analysis: comparing two sets of sequences | Single set motif enrichment analysis: comparing a set of sequences to a suitable background | Binned k-mer enrichment analysis | Use r Biocpkg("monaLisa") to annotate genomic regions with predicted motifs | Session info and logo | References

Introduction | Motif selection with Randomized Lasso Stability Selection | Load packages | Load dataset | Get TFBS per motif and peak | A note on collinearity | Identify important TFs | Session info and logo | References

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

Introduction | Preliminaries | Citing Rbowtie | Installation | Loading of Rbowtie | How to get help | Example usage for individual Rbowtie functions | Build the reference index with bowtie_build | Create alignment with bowtie | Create spliced alignment with SpliceMap | Session information | References