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AltAnalyze is an extremely user-friendly and open-source analysis toolkit that can be used for a broad range of genomics analyses. These analyses include the direct processing of raw RNASeq or microarray data files, advanced methods for single-cell population discovery, differential expression analyses, analysis of alternative splicing/promoter/polyadenylation and advanced isoform function prediction analysis (protein, domain and microRNA targeting). Multiple advanced visualization tools and à la carte analysis methods are supported in AltAnalyze (e.g., network, pathway, splicing graph). AltAnalyze is compatible with various data inputs for RNASeq data (FASTQ, BAM, BED), microarray platforms (Gene 1.0, Exon 1.0, junction and 3' arrays). This software requires no advanced knowledge of bioinformatics programs or scripting or advanced computer hardware. User friendly videos, online tutorials and blog posts are also available.
- 1.1 Program Description
- 1.2 Updates
- 1.3 Implementation
- 1.4 Requirements
- 1.5 Installation
- 1.6 Pre-Processing, External Files and Applications
- 1.7 Help with AltAnalyze
- 2.1 Where to Save Input Expression Files?
- 2.2 Running AltAnalyze from the Graphical User Interface
- 2.3 Running AltAnalyze from the Command-Line
- 2.4 AltAnalyze Analysis Options
- 2.5 Overview of Analysis Results
- 2.6 Additional à la carte Analyses
- 2.7 AltAnalyze Results Viewer
- 3.1 Default Methods
- 3.2 Algorithm Descriptions
- 3.3 Probe Set Filtering
- 3.4 Constitutive and Gene Expression Calculation
- 3.5 Alternative Splicing Prediction
- 3.6 Protein/RNA Inference Analysis
- 3.7 Gene Annotation Assignment
6 Building AltAnalyze Annotation Files
- 6.1 Splicing Annotations and Protein Associations
- 6.2 Building Ensembl-Exon Associations
- 6.3 Extracting UniProt Protein Domain Annotations Overview
- 6.4 Extracting Ensembl Protein Domain Annotations Overview
- 6.5 Extracting microRNA Binding Annotations Overview
- 6.6 Inferring Protein-Exon Associations Overview
- 6.7 Required Files for Manual Update
7 Evaluation of AltAnalyze Predictions