What's new in AltAnalyze 2.0.8.1
Jan 21, 2014
- Numerous bug fixes (listed in FeaturesToImplement),
- Multiple new accessory tools added: interactive network analysis and visualization, 3D PCA, identifier translator, alternative exon viewer, Venn Diagram viewer, and file merger,
- MarkerFinder algorithm included to unique find marker genes for each condition,
- Customizable hierarchical clustering visualization options and associated ontology/gene-set/gene correlation/filtering options ,
- WikiPathways visualization for inputs without gene-values,
- Batch effects normalization (combat),
- Support for Agilent Feature Extraction file normalization and analysis,
- Additional LineageProfiler analysis options,
- Network visualization and hierarchical clustering of GO-Elite results,
- Support for alternative input biological ID types,
- Addition of Whole Genome R Vista TF site predictions for GO-Elite. All features are available by command-line and GUI.
New in AltAnalyze 2.0.8 Dev 071713 (Jul 18, 2013)
- numerous bug fixes,
- multiple new accessory tools added: interactive network analysis and visualization, 3D PCA, identifier translator, alternative exon viewer, Venn Diagram viewer, and file merger,
- MarkerFinder algorithm included to unique find marker genes for each condition,
- customizable hierarchical clustering visualization options and associated ontology/gene-set/gene correlation/filtering options,
- WikiPathways visualization for inputs without gene-values,
- Batch effects normalization (combat),
- support for Agilent Feature Extraction file normalization and analysis,
- additional LineageProfiler analysis options,
- network visualization and hierarchical clustering of GO-Elite results and
- addition of Whole Genome R Vista TF site predictions for GO-Elite.
New in AltAnalyze 2.0.7 (Jun 14, 2012)
- moderated t-tests based based on the limma method,
- analysis of cell composition with the new program LineageProflier,
- robust quality control analysis and visualization,
- hierarchical and principal component analysis clustering/visualization,
- WikiPathways visualization,
- Additional Analyses menu added for streamlined access to visualization and pathway enrichment methods,
- bug fixes to 2.0.6 and
- more sensitive default RNA-Seq expression filtering options.
New in AltAnalyze 2.0.6 (Jan 20, 2012)
- Improved gene expression detection and filtering for RNA-Seq (separate RPKM and read-count filtering for exons and junctions).
- Improved constitutive exon-detection methods (introduced in database version Ensembl 64).
- Support added for the Affymetrix hGlue junction array
- New summary export result files (e.g., splicing-statistics for all analyzed features).
- New fully automated methods for AltAnalyze database creation (automated download of all necessary files - command-line only).
- Fixed several identified bugs from version 2.0.5 (e.g., problems with 3'array processing, Gene Ontology annotations, RNA-Seq import).
New in AltAnalyze 2.0.5 (Dec 20, 2011)
- Selection of multiple statistical p-value methods added (e.g., paired t-test, Mann Whitney) for all analyses (Section 2.4)
- New summary gene expression statistics file included (Section 2.5)
- Updated RNA-Seq gene-level RPKM calculations to provide more accurate gene expression estimates (Section 3.2)
- Gene expression estimates for RNA-Seq are now derived only from exon and not junction and exon expression (when applicable)
- Support of Affymetrix microRNA array annotation files added
- Protein coding potential and microRNA binding site annotations support added for conventional array data
- GO-Elite update, optimization and updated Ontology support
- Fixed import error on Windows machines for exon BED import from BEDTools