(0) Installation and Quick-Start | Installation | Creating and testing an example ompBAM-based package | To create an ompBAM-based package from within RStudio: | (1) Requirements to setting up a new R package to include ompBAM | (1a) Making a new package that compiles with ompBAM | (1b) Dependencies required to compile with ompBAM | (1c) Make Files | (1d) OpenMP compatibility | (2) Step-by-step guide to creating your first ompBAM-powered package | (2a) Headers and Includes | (2b) Sanity check for number of threads | (2c) Opening BAM files with ompBAM | Note 3 things: | (2d) Obtaining chromosome names and lengths | (2e) Constructing a loop to read the BAM file using ompBAM | (2f) Processing BAM reads using an OpenMP parallel FOR loop | (2g) Getting thread-specific reads from ompBAM | (2g:i) Checking "validity" of reads and "realizing" reads | (2h) Counting chromosome-specific reads | (2h:i) Obtaining the chromosome ID of each aligned read | (2h:ii) Tallying reads to a variable external to the parallel FOR loop | (2i) Closing the BAM file | (2j) Summarizing the tallied reads | (2k) Adding a progress bar | (3) pbam_in function documentation | (3a) Constructor | Usage | Parameters | Details | Examples | (3b) openFile() | (3c) SetInputHandle() | (3d) closeFile() | (3e) obtainChrs() | Return value | (3f) fillReads() | (3g) supplyRead() | (3h) remainingThreadReadsBuffer(); | (3i) Progress and File Size Functions | (4) pbam1_t function documentation | (4a) Constructor | (4b) validate() | (4c) realize() | (4d) isReal() | (4e) Getters of Read Core Data | (4f) Getters of Cigar Data | (4g) Getters of Alignment Sequence and Quality score | (4h) Tag Getters | (5) SessionInfo

Introduction | FAQ | Workflow from a glance | Quick-Start | Installation | Loading SpliceWiz | The SpliceWiz Graphics User Interface (GUI) | Navigating the GUI | Building the SpliceWiz reference | Process BAM files using SpliceWiz | Collate the experiment | Importing the experiment | Differential analysis | Assigning annotations to samples | Filtering high-confidence events | Performing differential analysis | Visualization | Volcano plots | Scatter plots | Gene ontology (GO) analysis | Heatmaps | SpliceWiz Coverage Plots | Coverage plots of individual samples | Normalized Coverage plots of individual samples | Group Coverage plots | Coverage plots using exon windows | Using the GUI | SessionInfo

Loading SpliceWiz | Reference Generation | Create a SpliceWiz reference from user-defined FASTA and GTF files locally | Prepare genome resources and building the reference as separate steps | Overwriting an existing reference, but using the same annotations | Create a SpliceWiz reference using web resources from Ensembl's FTP | Create a SpliceWiz reference using AnnotationHub resources | Create a SpliceWiz reference from species other than human or mouse | (NEW) Gene ontology annotations | STAR reference generation (using SpliceWiz wrappers) | Checking if STAR is installed | Building a STAR reference | Building a STAR genome without specifying gene annotations | Calculating Mappability Exclusions using STAR (optional) | Building BOTH STAR and SpliceWiz references together | Mappability exclusion generation using Rsubread | STAR alignment (using SpliceWiz wrappers) | Aligning a single sample using STAR | Aligning multiple samples using STAR | Finding FASTQ files recursively from a given directory | Processing BAM files | Creating COV files from BAM files without running processBAM | Converting COV files to BigWig | The OpenMP parameter explained | Collating the experiment | Downstream analysis using SpliceWiz | SessionInfo

0 Important announcement | 1 Installation | 2 Obtaining the example NxtIRF genome and gene annotation files | 3 Obtaining the example BAM file dataset for SpliceWiz | 4 Obtaining the Mappability Exclusion BED files | 5 Accessing NxtIRFdata via ExperimentHub | 5 Information about the example BAM files | SessionInfo