AltAnalyze Software Update History

note: For further details and explanation, see the associated sections in the full online AltAnalyze documentation.

Version 2.0.6 Updates

In this version, we improve upon changes made in the previous release and supply several new methods and analysis support. Changes include:

1. Improved gene expression detection and filtering for RNA-Seq (separate RPKM and read-count filtering for exons and junctions).
2. Improved constitutive exon-detection methods (introduced in database version Ensembl 64).
3. Support added for the Affymetrix hGlue junction array
4. New summary export result files (e.g., splicing-statistics for all analyzed features).
5. New fully automated methods for AltAnalyze database creation (automated download of all necessary files - command-line only).
6. Fixed several identified bugs from version 2.0.5 (e.g., problems with 3'array processing, Gene Ontology annotations, RNA-Seq import).

Version 2.0.5 Updates

New program features, improved methods and critical fixes to RNA-seq exon bed building bug for Windows:

1. Selection of multiple statistical p-value methods added (e.g., paired t-test, Mann Whitney) for all analyses (Section 2.4)
2. New summary gene expression statistics file included (Section 2.5)
3. Updated RNA-Seq gene-level RPKM calculations to provide more accurate gene expression estimates (Section 3.2)
4. Gene expression estimates for RNA-Seq are now derived only from exon and not junction and exon expression (when applicable)
5. Support of Affymetrix microRNA array annotation files added
6. Protein coding potential and microRNA binding site annotations support added for conventional array data
7. GO-Elite update, optimization and updated Ontology support
8. Fixed import error on Windows machines for exon BED import from BEDTools

Version 2.0.4 Updates

Critical fixes to bugs, resulting in program errors, introduced in version 2.03:

1. Running source-code on a remote machine now working
2. Independent analysis of exon only files (no junctions) now working
3. All species RNA-Seq databases will now load properly
4. More consistent results between exon only and exon with junction results (some novel exons missing or duplicated).
5. RNA-Seq and junction array splicing-index results for GO-Elite analysis will be properly written (no resulting GO-Elite error).

Version 2.0.3 Updates

New to version 2.03 AltAnalyze is support for both exon and junction RNASeq analysis, new functional annotations and normalization methods:

1. Support for RNASeq exon expression import from TopHat & BioScope (Section 1.5)
2. Support for platform independent exon/junction data in BED format (Section 1.5)
3. New independently confirmed exon and junction event report file (Section 2.5)
4. Updated species database support for RNASeq exon analyses (EnsMart62)
5. Optional quantile or RPKM normalization for exons and junctions (Section 3.2)
6. Addition of adjusted p-values for exon analyses (Section 3.2)
7. Addition of non-coding and nonsense mediated decay annotations (Section 3.6)
8. Identification of alternative poly-adenylation predictions (Section 3.5)
9. Addition of UniProt domain/motif exon-overlap annotations (Section 3.6)
10. Improved Ensembl gene function annotations (Section 3.7)
11. Fixed Cytoscape installation and extraction problems for Windows.
12. Automatic array recognition for version 4 format Affymetrix CEL files.
13. Memory optimization for import and analysis.

Version 2.02 Updates

1. Improved data import
2. Increased efficiency for datasets with many novel junction predictions (100k plus)
3. Options for removing junctions with both ends mapping to introns.

Version 2.01 Updates

New to version 2.01 AltAnalyze is support for junction aligned RNASeq data:

1. Support of Junction .BED file analysis (Sections 1.5, 2.4, 3.2 and 6.2)
2. Reciprocal junction analysis of RNASeq data (Section 2.4)
3. Over 50 species now supported for RNASeq reciprocal junction analysis (http://code.google.com/p/altanalyze/wiki/SupportedSpecies)
4. New miRNA target annotation databases added (Section 6.5)
5. Allows analysis of genes without constitutive evidence (Section 3.4)
6. Automatic analysis of up- and down-regulated genes by GO-Elite.
7. New automated tools for developers to create & update databases (Section 6.7)
8. New online RNASeq documentation (http://code.google.com/p/altanalyze)

Version 1.1.6 Updates

New to version 1.16 AltAnalyze is support for alternative splicing array types and decreased memory requirements:

1. Support of Affymetrix HJAY and MJAY arrays (Section 6.2)
2. Combined reciprocal junction and exon analysis for junction arrays (Section 2.3)
3. Better memory handling for FIRMA and protein domain analysis
4. Improved online support (http://code.google.com/p/altanalyze)

Version 1.1.5 Updates

New to version 1.15 AltAnalyze are new splicing algorithm options, new array support and improved DomainGraph connectivity. The main new features are:

1. Addition of FIRMA alternative exon analysis (Section 3.2)
2. Alternative exon analysis support for the Affymetrix Gene 1.0 array (Section 2.3)
3. Universal import of 3rd party alternative exon results for analysis (Section 3.2)
4. Restricted analysis of a pre-determined set of probe sets (Section 3.2)
5. Bundled integration of Cytoscape and DomainGraph (Sections 2.2 and 8)
6. Improved command-line options (Section 2.3)

Version 1.1.4 Updates

Several features have been added to AltAnalyze version 1.14. Please review these if you have used previous versions of AltAnalyze, since the method in which gene expression is evaluated for both gene expression and alternative exon analyses has been updated and will affect your results. The main new features are:

1. Updated Ensembl version 54 exon array annotations for constitutive gene probe sets (Section 3.4 and Section 6.2).
2. Support for core probe set only gene expression calculation (Section 3.4)
3. Improved filtering methods for gene expression data (Section 3.4).
4. Addition of advanced gene expression analysis statistics (Section 3.2).
5. Support for multi-group (>2) alternative exon analyses (Section 2.5).
6. GO-Elite support for adjusted p-value filtering optional settings (Section 3.2).
7. Improved automatic array type identification.
8. More streamlined graphical user interface options.