DEGreport News CHANGES IN DEGreport 1.15.4 2017-03-27 Lorena Pantano 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 2017-01-08 Lorena Pantano 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 2017-11-13 Lorena Pantano Fix: Add checking point in degPCA Feature: Add function to plot basic expression signatures. CHANGES IN DEGreport 1.13.12 2017-10-11 Lorena Pantano 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 2017-09-22 Lorena Pantano 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 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 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 Feature: Add degPCA plot from Rory Kirchner CHANGES IN DEGreport 1.13.5 2017-05-30 Lorena Pantano Feature: Accept matrix for degWidePlot CHANGES IN DEGreport 1.13.4 2017-05-22 Lorena Pantano 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 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 Feature: add degFilter to filter genes by group CHANGES IN DEGreport 1.13.1 2017-04-27 Lorena Pantano 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 Fix: Add new contributor CHANGES IN DEGreport 1.11.6 2017-04-07 Lorena Pantano Feature: Add function to plot genes in a wide format CHANGES IN DEGreport 1.11.4 02-17-2017 Lorena Pantano Feature: Re-organize vignette. Feature: Ignore warnings when plotting Feature: Improve volcano plot CHANGES IN DEGreport 1.11.3 01-03-2017 Lorena Pantano 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 Features: Add degCheckFactors functions to plot sizefactors used to normalize count data. CHANGES IN DEGreport 1.11.1 10-18-2016 Lorena Pantano Fixes: print clusterProfiler output. CHANGES IN DEGreport 1.9.9 10-14-2016 Lorena Pantano Fixes: Fix the reduccion of clusters to use correlation values directly. CHANGES IN DEGreport 1.9.9 10-06-2016 Lorena Pantano Fixes: GO enrichment function. Input genes was wrong. CHANGES IN DEGreport 1.9.7 07-29-2015 Lorena Pantano 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 FIX SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG CHANGES IN DEGreport 1.01.01 10-17-2014 Lorena Pantano FIX BUG WHEN ONLY ONE GENE IS DEG CHANGES IN DEGreport 0.99.12 09-04-2014 Lorena Pantano CORRECT DOC OF createReport CHANGES IN DEGreport 0.99.11 09-02-2014 Lorena Pantano ADD ncores TO REPORT CREATION CHANGES IN DEGreport 0.99.10 08-16-2014 Lorena Pantano REMOVE BIOMART FROM VIGNETTES DUE TO WINDOWS UNKNOWN BUILD ISSUES CHANGES IN DEGreport 0.99.9 08-02-2014 Lorena Pantano ADDING PARALLELIZATION TO BAYESIAN INFERENCE CHANGES IN DEGreport 0.99.4 05-19-2014 Lorena Pantano CODING STYLE * replacing tab by 4 spaces * cleaning up function * adding unit tests