AltAnalyze Changelog

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