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Bioconductor Changlog.
Tue, 13 Oct 2009
oneChannelGUI
Changed exprSet to ExpressionSet in code comments to reflect changes in code.
[/oneChannelGUI] permanent link
oneChannelGUI
Adding Alternative splicing visualization for one gene-level probeset
Adding conversion, for exon arrays, from gene-level probe set to genebank accession number
Extending to exon arrays, limma topTable, the possibility to create template A for Ingenuity Knowledge Base
Adding a filter to subset alternative splicing events using MiDAS p-values/RP p-values/average mean SI difference
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oneChannelGUI
Adding the possibility to update gene/exon Affymetrix library files by affyCompatible library.
Adding the possiiblity to add EGs to tab delimited files produced by oneChannelGUI implementaiton of limma, RankProd and siggene
Fixing some bugs on GOenrichment using Affymetrix exon arrays.
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oneChannelGUI
Added a routine to load ILLUMINA arrays starting from BeadStudio v.1 and 2 output.
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oneChannelGUI
Updated internal exon annotation.
Refined filtering functions to be used for exon-level analysis.
Added function for direct loading of affymetrix library files and location of apt tools directory
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oneChannelGUI
Fix a bug in uploading tab delimited files.
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oneChannelGUI
adding missing helps
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oneChannelGUI
Affymetrix library files for exon array analysis are directly downloaded, the first time user performs a exon array analysis.
Affymetrix library files and APT tools folders location are stored in the /oneChannelGUI/etc/LocalData.txt and can be updated and modified by the user
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oneChannelGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
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oneChannelGUI
Correcting little bugs in limma Toptable for Illumina data
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oneChannelGUI
Added GUI biocView to DESCRIPTION file.
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oneChannelGUI
Setting gene-level annotation for genechip EXON 1.0 ST using org.XX.db and exon-level annotation via biomaRt.
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oneChannelGUI
Added Cosie method to correct SI index: Gaidatzis et al. Nucleic Acids Research, 2009, pg. 1.
Alternative splicing events can be visualized on the UCSC Genome Browser via rtracklayer.
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oneChannelGUI
fixing a bug in data loading
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oneChannelGUI
Fixing a bug in extracting probe set ids from GO term
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oneChannelGUI
Removing a bug related to limma topTable generation with annotation using yeast2 arrays
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oneChannelGUI
Fixing a bug, UNIX systems, related to the saving of unfiltered data produced by filtering menu functions
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oneChannelGUI
Adding a QC for raw data for genechip EXON 1.0 ST:
Using APT tools positive and negative control probes, i.e. exon and introns of known housekeeping genes, are extracted form the CEL files, log2 transformed and plotted to give an idea of the array signals.
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oneChannelGUI
Standardizing reference to Artistic License 2.0.
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oneChannelGUI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
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oneChannelGUI
fixing malformed description
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oneChannelGUI
fixing a bug in illumina data loading
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oneChannelGUI
fixing bug in RP exon filtering
fixing a bug in alternative splicing filtering
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oneChannelGUI
fixing bugs in handling db annotation packages
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oneChannelGUI
Fixing a bug in gene and exon level data loading
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oneChannelGUI
Deep update of tools for detecting variant exons upon statistical detection of alternative splicing events.
Fixing a bug in normalization of illumina data
[/oneChannelGUI] permanent link
oneChannelGUI
Adding a filter for exon-level analysis for geneChipEXON 1.0 ST arrays. ThebiomartFilter uses biomaRt to subset only those gene-level probe sets associated to an entrez Gene ID linked to more than one ensembl transcripts. This filter will limit alternative splicing detection only on annotated alternative spliced transcripts.
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oneChannelGUI
Fixing some bugs in the use of annotation db packages.
Optimizing exon-level genechips EXON 1.0 analysis:
Exon-level filters now produce a file with the list of significantly detected exons. Graphs associated to alternative splicing inspection were simplified. The function Mapping exon-level probesets to RefSeq now uses a list of exons considered significantly alternatively spliced derived from exon-level filters.
[/oneChannelGUI] permanent link
oneChannelGUI
Added Cosie method to correct SI index: Gaidatzis et al. Nucleic Acids Research, 2009, pg. 1.
Alternative splicing events can be visualized on the UCSC Genome Browser via rtracklayer.
[/oneChannelGUI] permanent link
oneChannelGUI
fixed Rdversion 2 parser warnings
[/oneChannelGUI] permanent link
oneChannelGUI
fixing a code bug
[/oneChannelGUI] permanent link
oneChannelGUI
Fixing a warning on manual documentation
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oneChannelGUI
Fixing a typing error in man Rd name
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oneChannelGUI
Limma added as tool for alternative splicing detection
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oneChannelGUI
Changed biocViews entry of Statistics to Bioinformatics.
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oneChannelGUI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
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oneChannelGUI
Fixing bugs on routine for direct loading of gene/exon affy library files needed for APT tools usage.
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oneChannelGUI
Adding missing man files
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