DEGreport News

CHANGES IN DEGreport 1.13.12
    2017-10-11  Lorena Pantano <lorena.pantano@gmail.com>
   
   Feature: Return scatter plots between PCs and metadata in degCovariates.
   Feature: Use ConsensusClusterPlus to cluster genes with degPatterns.

CHANGES IN DEGreport 1.13.11
    2017-09-22  Lorena Pantano <lorena.pantano@gmail.com>
   
   Feature: significant works with DESeqResults class.
   Fix: log2 in degPlot wasn't active.
   Feature: Allow plot samples together or not in degCheckFactor.
   Feature: Migrate vignette to new BiocStyle.
   Fix: Automatic QC report. Reduce final report with most important figures.
   
CHANGES IN DEGreport 1.13.10
    2017-09-07  Lorena Pantano <lorena.pantano@gmail.com>
    
    Fix: Complete vignette with new functions.
    Feature: Add DEGSet construct to accept other sources.
    Feature: Adapt degQC to accept DEGSet object.
    Feature: Allow multiple group for degMB and degVB.
    Feature: Add optional log2 for gene plotting.
    Feature: Plot correlation of shrunken vs unshruken log2fc.
    Feature: Allow to plot original MA plot.
    Feature: Adapt summary of DESeq2Results to data.frame and compatible with
             markdown output, and multiple alpha values.
    Fix: links in man pages.
    Feature: Pass options to Heatmap in degCorCov.@vbarrera.
    Feature: Add parameter to select top rows from DEGset.
    Fix: Change method names to short words.
    Feature: degVolcano accepts DESeq2Results class.
    Fix: degPCA print the correct PC number on x/ylabels.
    Fix: Move NEWS to parent folder.
    Feature: Add method to get significant genes from DEGSet class.
    Feature: Add plotMA method to show shrunken effect. @vbarrera
    Fix: Move to testthat for examples.
    Feature: Adding main class and methods to handle DEG output.
    Fix: axis in degPCA now show the values.
    Feature: Handle multiple contrasts/coefficient for DESeq2 results.
    
CHANGES IN DEGreport  1.13.7
    2017-08-08  Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: new function to analyze the correlation
             among covaritaes in metatdata
    Deprecation: all functions related to foldchange accuraty are removed. 
                 Using lfcShrink much better now
    Style: Add more unit tests
    Feature: Accept SE like objects to degPlot and
             use better gene names if rowData has it
    Feature: Use plot_grid for degPattern and save plot
    Feature: Use text or point in degPCA
    Feature: Fix labels of degPlot
    Feature: Accept matrix in degPlot
    Fix: correctly handling rowData in SE objects for degPlot
    Fix: plot only legend if group > 1
    Feature: More output for degPattern
    Style: change to lower-cases inside degCovariates function

CHANGES IN DEGreport  1.13.6
    2017-05-30  Lorena Pantano <lorena.pantano@gmail.com>

    Feature: Add degPCA plot from Rory Kirchner
   
CHANGES IN DEGreport  1.13.5
    2017-05-30  Lorena Pantano <lorena.pantano@gmail.com>

    Feature: Accept matrix for degWidePlot
    
CHANGES IN DEGreport  1.13.4
    2017-05-22  Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: Add degCovariates to calculate correlations
             between PCs from count data and covariates
             from metadata

CHANGES IN DEGreport  1.13.3
    2017-05-19  Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: Add degMDS for PCA like clustering figures
    Feature: Add labels parameters to degPlot
    
CHANGES IN DEGreport  1.13.2
    2017-05-05  Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: add degFilter to filter genes by group

CHANGES IN DEGreport  1.13.1
    2017-04-27  Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: change arrange for plotQC plots with cowplot
    Feature: Use theme_minimal inside degResults
    Feature: Change title for some sections in degResults
    
CHANGES IN DEGreport 1.11.7

    2017-04-08 Lorena Pantano <lorena.pantano@gmail.com>
    
    Fix: Add new contributor

CHANGES IN DEGreport 1.11.6

    2017-04-07 Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: Add function to plot genes in a wide format

CHANGES IN DEGreport 1.11.4

    02-17-2017 Lorena Pantano <lorena.pantano@gmail.com>
    
    Feature: Re-organize vignette.
    Feature: Ignore warnings when plotting
    Feature: Improve volcano plot

CHANGES IN DEGreport 1.11.3

    01-03-2017 Lorena Pantano <lorena.pantano@gmail.com>
    
    Fix: fix order of clusters figures that are not in the correct
         place in some cases with many groups.


CHANGES IN DEGreport 1.11.2

    12-09-2016 Lorena Pantano <lorena.pantano@gmail.com>
    
    Features: Add degCheckFactors functions to plot sizefactors used to
              normalize count data.

CHANGES IN DEGreport 1.11.1

    10-18-2016 Lorena Pantano <lorena.pantano@gmail.com>
    
    Fixes: print clusterProfiler output.

CHANGES IN DEGreport 1.9.9

    10-14-2016 Lorena Pantano <lorena.pantano@gmail.com>
    
    Fixes: Fix the reduccion of clusters to use correlation
           values directly.

CHANGES IN DEGreport 1.9.9

    10-06-2016 Lorena Pantano <lorena.pantano@gmail.com>
    
    Fixes: GO enrichment function. Input genes was wrong.
    
CHANGES IN DEGreport 1.9.7
    
    07-29-2015 Lorena Pantano <lorena.pantano@gmail.com>

    Features: Add functions to return markdown report from DESeq2 object,
              and clustering function for time course data.
    Fixes: small bugs related to Nan values or small diversity values
           in QC plots.

CHANGES IN DEGreport 1.4.0
    
    07-03-2015 Lorena Pantano <lorena.pantano@gmail.com>

    FIX SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG

CHANGES IN DEGreport 1.01.01
    
    10-17-2014 Lorena Pantano <lorena.pantano@gmail.com>

    FIX BUG WHEN ONLY ONE GENE IS DEG

CHANGES IN DEGreport 0.99.12
    
    09-04-2014 Lorena Pantano <lorena.pantano@gmail.com>

    CORRECT DOC OF createReport

CHANGES IN DEGreport 0.99.11
    
    09-02-2014 Lorena Pantano <lorena.pantano@gmail.com>

    ADD ncores TO REPORT CREATION

CHANGES IN DEGreport 0.99.10
    
    08-16-2014 Lorena Pantano <lorena.pantano@gmail.com>

    REMOVE BIOMART FROM VIGNETTES DUE TO WINDOWS UNKNOWN BUILD ISSUES

CHANGES IN DEGreport 0.99.9
    
    08-02-2014 Lorena Pantano <lorena.pantano@gmail.com>

    ADDING PARALLELIZATION TO BAYESIAN INFERENCE

CHANGES IN DEGreport 0.99.4
    
    05-19-2014 Lorena Pantano <lorena.pantano@gmail.com>

    CODING STYLE
    * replacing tab by 4 spaces
    * cleaning up function
    * adding unit tests
