IsoformSwitchAnalyzeR11 months ago
Abstract | Table of Content | Preliminaries | Background and Package Description | Installation | How To Get Help | What To Cite | Quick Start | Overview of Isoform Switch Workflow | Example Workflow | Importing the Data | Part 1 | Part 2 | Examples Visualizations | The switchPlot | Genome-wide Summaries | Consequence Enrichment Analysis | Splicing Enrichment Analysis | Overview Plots | Detailed Workflow | Overview of Detailed Workflow | IsoformSwitchAnalyzeR Background Information | The switchAnalyzeRlist | Function overview | Importing Data Into R | Importing Data from Kallisto, Salmon, RSEM or StringTie | Importing Data from Salmon via Tximeta | Importing Data from Cufflinks/Cuffdiff | Importing Data from Full-length Transcript Assemblers | Filtering | Identifying Isoform Switches | Testing for Isoform Switches via DEXSeq | Testing for Isoform Switches via satuRn | Testing for Isoform Switches with other Tools | Analyzing Open Reading Frames | Analyzing Only Known Isoforms | Analyzing Known and Novel Isoforms | Analyzing Only Novel Isoforms | Extracting Nucleotide and Amino Acid Sequences | Advice for Running External Sequence Analysis Tools and Downloading Results | Importing External Sequence Analysis | Predicting Alternative Splicing | Predicting Switch Consequences | Post Analysis of Isoform Switches with Consequences | Analysis of Individual Isoform Switching | Genome-Wide Analysis of Isoform Switching | Other Tools in IsoformSwitchAnalyzeR | Analyzing Alternative Splicing | Overview of Alternative Splicing Workflow | Genome-Wide Analysis of Alternative Splicing | Interoperability with Other Tools | pairedGSEA | Importing results from pairedGSEA | Exporting data to pairedGSEA | Other workflows | Applying on Long-read Sequencing Data | Applying on Single-cell Sequencing Data | Augmenting ORF Predictions with Pfam Results | Analyze Small Upstream ORFs | Remove Sequences Stored in SwitchAnalyzeRlist | Adding Uncertain Category to Coding Potential Predictions | Quality control of ORF of known annotation | Analyzing the Biological Mechanisms Behind Isoform Switching | Analyzing experiments without replicates | Rescue StringTie Annoation and Extract Gene Count Matrix | Frequently Asked Questions, Problems and Errors | FAQ Table of Content | What Quantification Tool(s) Should I Use? | What Transcript Database Should I Use? | Are there Different Approaches to Analysis of Alternative Splicing? | Approach 1: Exon based analysis | Approach 2: Splicing based analysis | Approach 3: Transcript based analysis | How to handle confounding effects (including batches) | What constitute an independent biological replicate? | Adding differential gene expression | The error "The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (Jaccard similarity < 0.925)" | The warning "The annotation and quantification (count/abundance matrix and isoform annotation) seem to be slightly different" | The error "The supplied design matrix will result in a model matrix that is not full rank" | How to prevent visualization of NMD in the switchPlot | BSGenomes for non-model organisms | The switchPlot contains regions "Not Annotated" | Can I use a GFF file instead of a GTF file? | Can I use quantificaiton files from Galaxy? | Final Remarks | Sessioninfo | Generating additional links for sharing online