DEGreport News CHANGES IN DEGreport 1.41.1 * made that the sequence of clusters in the dendogram matches the sequence of clusters in the trajectories @zellerivo * Fix error in check report about stack limit size * Add option to avoid running dendextend https://github.com/lpantano/DEGreport/issues/62 CHANGES IN DEGreport 1.39.3 * Add ctb CHANGES IN DEGreport 1.39.1 * merging changes from 1.38.1 CHANGES IN DEGreport 1.38.1 * remove lasso and fdrtools * merge https://github.com/lpantano/DEGreport/pull/56 CHANGES IN DEGreport 1.33.2 * Remove lasso2 from dependencies CHANGES IN DEGreport 1.33.1 * Remove Nozzle.R1 from dependencies CHANGES IN DEGreport 1.31.6 * Migrate gather to pitvot_longer * Fix warning in melt in degcovariates * Fix significants function, issue with !!!sym CHANGES IN DEGreport 1.31.3 * Fix error in example when using `head` after pipe CHANGES IN DEGreport 1.27.1 * Fix: Export n() from dplyrs.[#27](https://github.com/lpantano/DEGreport/issues/27#issuecomment-819201968) CHANGES IN DEGreport 1.25.3 * Feature: degPlot accepts sizePoint as parameter to indicate the size of the plotted points. CHANGES IN DEGreport 1.25.2 * Fix: In the case of non-correlation avoid error in significants code. @vbarrera and @mjsteinbaugh * Feature: degCovariates shows grey stroke for variables with p-value < 0.05 from the first correlation step. @vbarrera CHANGES IN DEGreport 1.25.1 * Feature: degPlot will keep the gene order given by the user. CHANGES IN DEGreport 1.23.3 * Fix: pass min_counts parameter to degPlotCluster CHANGES IN DEGreport 1.23.2 * Fix: adopt class(counts)[1] to check classes CHANGES IN DEGreport 1.23.1 * Feature: add prefix to clusters plot in `degPlotCluster` CHANGES IN DEGreport 1.21.2 * Feature: add `scale` option to degSignature * Feature: add lfdr support from fdrtools to degCombs and DEGSet object. 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