Changes in version 1.45.1 o Fixed labs() function calls in multiple R files: - methods.R (2 occurrences in degMean and degVar functions) - clustering.R (2 occurrences) - volcanoPlot.R (1 occurrence) Changes in version 1.41.1 o made that the sequence of clusters in the dendogram matches the sequence of clusters in the trajectories @zellerivo o Fix error in check report about stack limit size o Add option to avoid running dendextend https://github.com/lpantano/DEGreport/issues/62 Changes in version 1.39.3 o Add ctb Changes in version 1.39.1 o merging changes from 1.38.1 Changes in version 1.38.1 o remove lasso and fdrtools o merge https://github.com/lpantano/DEGreport/pull/56 Changes in version 1.33.2 o Remove lasso2 from dependencies Changes in version 1.33.1 o Remove Nozzle.R1 from dependencies Changes in version 1.31.6 o Migrate gather to pitvot_longer o Fix warning in melt in degcovariates o Fix significants function, issue with !!!sym Changes in version 1.31.3 o Fix error in example when using `head` after pipe Changes in version 1.27.1 o Fix: Export n() from dplyrs.[#27](https://github.com/lpantano/DEGreport/issues/27#issuecomment-819201968) Changes in version 1.25.3 o Feature: degPlot accepts sizePoint as parameter to indicate the size of the plotted points. Changes in version 1.25.2 o Fix: In the case of non-correlation avoid error in significants code. @vbarrera and @mjsteinbaugh o Feature: degCovariates shows grey stroke for variables with p-value < 0.05 from the first correlation step. @vbarrera Changes in version 1.25.1 o Feature: degPlot will keep the gene order given by the user. Changes in version 1.23.3 o Fix: pass min_counts parameter to degPlotCluster Changes in version 1.23.2 o Fix: adopt class(counts)[1] to check classes Changes in version 1.23.1 o Feature: add prefix to clusters plot in `degPlotCluster` Changes in version 1.21.2 o Feature: add `scale` option to degSignature o Feature: add lfdr support from fdrtools to degCombs and DEGSet object. Changes in version 1.21.1 o Fix: call summary from DESeq2 o Fix: degPlot to avoid reordering `ann` vector when checking if they exists. o Fix: degSignature to work with new version of melt. o Fix: degVolcano doesn't uses ranges of 0.5 in the x axis anymore o Fix: degMA used always raw table, now fixed to use the right one. Changes in version 1.19.2 o Fix: Error when metadata doesn't contain group column. Thanks to @hexaflexa. o Fix: Update documentation link in degComb. o Fix: Fix error when factor has extra-levels by @roryk. o Fix: Fix cutoff summary in degPattern. Changes in version 1.19.1 o Feature: Accept data.frame to plot custom clusters. o Feature: Add cluster consistency plot to degPattern. Changes in version 1.17.8 o Fix: typo in as.DEGSet from DESeq2 object. Changes in version 1.17.7 o Fix: re-format NEWS file Changes in version 1.17.6 o Fix: Error in degCovariate when no correlation exists. Changes in version 1.17.5 o Fix: Fix documentation warning. Changes in version 1.17.4 o Feature: Reduce parameter is used to remove outlier points after clustering genes. o Feature: Add maximum log2FoldChange to the significance output when multiple comparisons are used as inputs. o Feature: Remove non-mapped genes in degPlot. o Feature: Add specific function to plot degPatterns clusters. o Fix: Support DESeqResults for list of DEGSets. o Feature: Add variable selection for covariates that correlate with PCs in degCovariate function. o Feature: Add lasso as an option to variable selection in covariate analysis. o Feature: Fill with colors only significant variables by lm or lasso, and draw borber for correlated variables by cor.test. Changes in version 1.17.3 o Fix: degCovariates works with metadata only with numerical variables o * Feature: Improve support for DEGSet conversion. o Fix: Remove theme set up for degPCA plot. o Feature: Make function to generate colors for metadata variables for annotation column in heatmap figure. o Feature: Improve degCovariates to add effect size of the covariates. Thanks to @vbarrera o Fix: Improve degCovariates man pages. Changes in version 1.17.1 o Fix: remove discrete scale color in degPCA. o Feature: Return same output for degPatterns with single genes. Thanks Amir Jassim. o Feature: Allow custom y-axis lab in degPlot. Thanks @vbarrera. Changes in version 1.15.4 o Fix: * Fix typo in variable inside degClean o Fix: Remove all columsn with NA values in degClean o Feature: Plot only when degPatterns has only one gene. Thanks Amir Jassim. o Feature: Add geom_cor to plot correlation values to a ggplot2 plot. o Feature: Add eachStep option to degPattern to apply groupDifference to each time point and not only to the maximum and minimum values. o Feature: Add covariates dendograme to degCovariates. o Fix: Wrong matrix in degPattern. Thanks Amir Jassim. o Feature: Add option to filter genes in degPattern. Thanks Amir Jassim. o Feature: Return raw and summarise table in degPattern o Feature: Migrate to rmarkdown for vignette o Feature: Return prcomp output when using degPCA o Fix: Typo in degPattern function, and set up to FALSE the use of consensusCluster. o Fix: degPlot to be able to work with one gene. o Feature: Add the option to look for specific patterns, or genes as reference. o Feature: Return scaled values if scale==TRUE in degPattern. o Feature: Add values used in plots for degPattern function. Thanks to Amir Jassim. o 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 version 1.15.2 o Feature: Add support to list for significant and recover full table. o Feature: Add support to different shrinkage estimator. o Fix: Volcano plot was plotting wrong the shadows in the y-axis. o Fix: Use correct option in DESeq2::results to count UP/DOWN genes. o Feature: Allow to ask for up/down genes. Thanks to Radhika Khetani. Changes in version 1.15.1 o Fix: Add checking point in degPCA o Feature: Add function to plot basic expression signatures. Changes in version 1.13.12 o Fix: * Fix NA values in covariates analysis and add pvalue-ploting o Fix: Avoid error when none covariate is significant o Feature: Return scatter plots between PCs and metadata in degCovariates. o Feature: Use ConsensusClusterPlus to cluster genes with degPatterns. Changes in version 1.13.11 o Feature: significant works with DESeqResults class. o Fix: log2 in degPlot wasn't active. o Feature: Allow plot samples together or not in degCheckFactor. o Feature: Migrate vignette to new BiocStyle. o Fix: Automatic QC report. Reduce final report with most important figures. Changes in version 1.13.10 o Fix: Complete vignette with new functions. o Feature: Add DEGSet construct to accept other sources. o Feature: Adapt degQC to accept DEGSet object. o Feature: Allow multiple group for degMB and degVB. o Feature: Add optional log2 for gene plotting. o Feature: Plot correlation of shrunken vs unshruken log2fc. o Feature: Allow to plot original MA plot. o Feature: Adapt summary of DESeq2Results to data.frame and compatible with markdown output, and multiple alpha values. o Fix: links in man pages. o Feature: Pass options to Heatmap in degCorCov.@vbarrera. o Feature: Add parameter to select top rows from DEGset. o Fix: Change method names to short words. o Feature: degVolcano accepts DESeq2Results class. o Fix: degPCA print the correct PC number on x/ylabels. o Fix: Move NEWS to parent folder. o Feature: Add method to get significant genes from DEGSet class. o Feature: Add plotMA method to show shrunken effect. @vbarrera o Fix: Move to testthat for examples. o Feature: Adding main class and methods to handle DEG output. o Fix: axis in degPCA now show the values. o Feature: Handle multiple contrasts/coefficient for DESeq2 results. Changes in version 1.13.7 o 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 o Feature: Accept SE like objects to degPlot and use better gene names if rowData has it o Feature: Use plot_grid for degPattern and save plot o Feature: Use text or point in degPCA o Feature: * Fix labels of degPlot o Feature: Accept matrix in degPlot o Fix: correctly handling rowData in SE objects for degPlot o Fix: plot only legend if group > 1 o Feature: More output for degPattern o Style: change to lower-cases inside degCovariates function Changes in version 1.13.6 o Feature: Add degPCA plot from Rory Kirchner Changes in version 1.13.5 o Feature: Accept matrix for degWidePlot Changes in version 1.13.4 o Feature: Add degCovariates to calculate correlations between PCs from count data and covariates from metadata Changes in version 1.13.3 o Feature: Add degMDS for PCA like clustering figures o Feature: Add labels parameters to degPlot Changes in version 1.13.2 o Feature: add degFilter to filter genes by group Changes in version 1.13.1 o Feature: change arrange for plotQC plots with cowplot o Feature: Use theme_minimal inside degResults o Feature: Change title for some sections in degResults Changes in version 1.11.7 o Fix: Add new contributor Changes in version 1.11.6 o Feature: Add function to plot genes in a wide format Changes in version 1.11.4 o Feature: Re-organize vignette. o Feature: Ignore warnings when plotting o Feature: Improve volcano plot Changes in version 1.11.3 o Fix: * Fix order of clusters figures that are not in the correct place in some cases with many groups. Changes in version 1.11.2 o Features: Add degCheckFactors functions to plot sizefactors used to normalize count data. Changes in version 1.11.1 o Fixes: print clusterProfiler output. Changes in version 1.9.9 o Fixes: * Fix the reduccion of clusters to use correlation values directly. o Fixes: GO enrichment function. Input genes was wrong. Changes in version 1.9.7 o Features: Add functions to return markdown report from DESeq2 object, and clustering function for time course data. o Fixes: small bugs related to Nan values or small diversity values in QC plots. Changes in version 1.4.0 o Fix SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG Changes in version 1.01.01 o Fix BUG WHEN ONLY ONE GENE IS DEG Changes in version 0.99.12 o CORRECT DOC OF createReport Changes in version 0.99.11 o ADD ncores TO REPORT CREATION Changes in version 0.99.10 o REMOVE BIOMART FROM VIGNETTES DUE TO WINDOWS UNKNOWN BUILD ISSUES Changes in version 0.99.9 o ADDING PARALLELIZATION TO BAYESIAN INFERENCE Changes in version 0.99.4 o replacing tab by 4 spaces o cleaning up function o adding unit tests