DEGreport News

CHANGES IN DEGreport 1.21.1
    * Fix: call summary from DESeq2
    * Fix: degPlot to avoid reordering `ann` vector when checking if they exists.
    * Fix: degSignature to work with new version of melt.
    * Fix: degVolcano doesn't uses ranges of 0.5 in the x axis anymore
    * Fix: degMA used always raw table, now fixed to use the right one.

CHANGES IN DEGreport 1.19.2

    * Fix: Error when metadata doesn't contain group column. Thanks to @hexaflexa.
    * Fix: Update documentation link in degComb.
    * Fix: Fix error when factor has extra-levels by @roryk.
    * Fix: Fix cutoff summary in degPattern.

CHANGES IN DEGreport 1.19.1

    * Feature: Accept data.frame to plot custom clusters.
    * Feature: Add cluster consistency plot to degPattern.

CHANGES IN DEGreport 1.17.8

    * Fix: typo in as.DEGSet from DESeq2 object.

CHANGES IN DEGreport 1.17.7

    * Fix: re-format NEWS file
    
CHANGES IN DEGreport 1.17.6

    * Fix: Error in degCovariate when no correlation exists.

CHANGES IN DEGreport 1.17.5

    * Fix: Fix documentation warning.

CHANGES IN DEGreport 1.17.4
    
    * Feature: Reduce parameter is used to remove outlier points
             after clustering genes.
    * Feature: Add maximum log2FoldChange to the significance output
             when multiple comparisons are used as inputs.
    * Feature: Remove non-mapped genes in degPlot.
    * Feature: Add specific function to plot degPatterns clusters.
    * Fix: Support DESeqResults for list of DEGSets.
    * Feature: Add variable selection for covariates that correlate with PCs
             in degCovariate function.
    * Feature: Add lasso as an option to variable selection in covariate
             analysis.
    * Feature: Fill with colors only significant variables by lm or lasso, and 
             draw borber for correlated variables by cor.test.

CHANGES IN DEGreport 1.17.3

        * Fix: degCovariates works with metadata only with numerical variables
        * * Feature: Improve support for DEGSet conversion.
        * Fix: Remove theme set up for degPCA plot.
        * Feature: Make function to generate colors for metadata variables for
                 annotation column in heatmap figure.
        * Feature: Improve degCovariates to add effect size of the covariates.
                 Thanks to @vbarrera
        * Fix: Improve degCovariates man pages.

CHANGES IN DEGreport 1.17.1

        * Fix: remove discrete scale color in degPCA.
        * Feature: Return same output for degPatterns with single genes. Thanks Amir Jassim.
        * Feature: Allow custom y-axis lab in degPlot. Thanks @vbarrera.


CHANGES IN DEGreport 1.15.4

        * Fix: * Fix typo in variable inside degClean
        * Fix: Remove all columsn with NA values in degClean
        * Feature: Plot only when degPatterns has only one gene. Thanks Amir Jassim.
        * Feature: Add geom_cor to plot correlation values to a ggplot2 plot.
        * Feature: Add eachStep option to degPattern to apply groupDifference
          to each time point and not only to the maximum and minimum values.
        * Feature: Add covariates dendograme to degCovariates.
        * Fix: Wrong matrix in degPattern. Thanks Amir Jassim.
        * Feature: Add option to filter genes in degPattern. Thanks Amir Jassim.
        * Feature: Return raw and summarise table in degPattern
        * Feature: Migrate to rmarkdown for vignette
        * Feature: Return prcomp output when using degPCA
        * Fix: Typo in degPattern function, and set up to FALSE the
          use of consensusCluster.
        * Fix: degPlot to be able to work with one gene.
        * Feature: Add the option to look for specific patterns, or genes as
            reference.
        * Feature: Return scaled values if scale==TRUE in degPattern.
        * Feature: Add values used in plots for degPattern function. Thanks to Amir Jassim.
        * Feature: Get significants for a list of DEGSet objects binding
             the tables first, calculating a new FDR,
             and aplying the filter as last step.
             https://support.bioconductor.org/p/104059/#104072
             
CHANGES IN DEGreport 1.15.2

    * Feature: Add support to list for significant and recover full table.
    * Feature: Add support to different shrinkage estimator.
    * Fix: Volcano plot was plotting wrong the shadows in the y-axis.
    * Fix: Use correct option in DESeq2::results to count UP/DOWN genes.
    * Feature: Allow to ask for up/down genes. Thanks to Radhika Khetani.

CHANGES IN DEGreport 1.15.1

    * Fix: Add checking point in degPCA
    * Feature: Add function to plot basic expression signatures.

CHANGES IN DEGreport 1.13.12

   * Fix: * Fix NA values in covariates analysis and add pvalue-ploting
   * Fix: Avoid error when none covariate is significant
   * Feature: Return scatter plots between PCs and metadata in degCovariates.
   * Feature: Use ConsensusClusterPlus to cluster genes with degPatterns.

CHANGES IN DEGreport 1.13.11

   * 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

    * 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

    * 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

    * Feature: Add degPCA plot from Rory Kirchner
   
CHANGES IN DEGreport  1.13.5

    * Feature: Accept matrix for degWidePlot
    
CHANGES IN DEGreport  1.13.4

    * Feature: Add degCovariates to calculate correlations
             between PCs from count data and covariates
             from metadata

CHANGES IN DEGreport  1.13.3

    * Feature: Add degMDS for PCA like clustering figures
    * Feature: Add labels parameters to degPlot
    
CHANGES IN DEGreport  1.13.2

    * Feature: add degFilter to filter genes by group

CHANGES IN DEGreport  1.13.1

    * 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

    * Fix: Add new contributor

CHANGES IN DEGreport 1.11.6

    * Feature: Add function to plot genes in a wide format

CHANGES IN DEGreport 1.11.4

    * Feature: Re-organize vignette.
    * Feature: Ignore warnings when plotting
    * Feature: Improve volcano plot

CHANGES IN DEGreport 1.11.3

    * 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

    * Features: Add degCheckFactors functions to plot sizefactors used to
              normalize count data.

CHANGES IN DEGreport 1.11.1

    * Fixes: print clusterProfiler output.

CHANGES IN DEGreport 1.9.9

    * Fixes: * Fix the reduccion of clusters to use correlation
           values directly.

CHANGES IN DEGreport 1.9.9

    * Fixes: GO enrichment function. Input genes was wrong.
    
CHANGES IN DEGreport 1.9.7
    
    * 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
    
    * Fix SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG

CHANGES IN DEGreport 1.01.01
    
    * Fix BUG WHEN ONLY ONE GENE IS DEG

CHANGES IN DEGreport 0.99.12
    
    * CORRECT DOC OF createReport

CHANGES IN DEGreport 0.99.11
    
    * ADD ncores TO REPORT CREATION

CHANGES IN DEGreport 0.99.10
    
    * REMOVE BIOMART FROM VIGNETTES DUE TO WINDOWS UNKNOWN BUILD ISSUES

CHANGES IN DEGreport 0.99.9
    
    * ADDING PARALLELIZATION TO BAYESIAN INFERENCE

CHANGES IN DEGreport 0.99.4
    

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