NEWS

---

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

DEGreport 1.39.3

• Add ctb

DEGreport 1.39.1

• merging changes from 1.38.1

DEGreport 1.38.1

• remove lasso and fdrtools
• merge https://github.com/lpantano/DEGreport/pull/56

DEGreport 1.33.2

• Remove lasso2 from dependencies

DEGreport 1.33.1

• Remove Nozzle.R1 from dependencies

DEGreport 1.31.6

• Migrate gather to pitvot_longer
• Fix warning in melt in degcovariates
• Fix significants function, issue with !!!sym

DEGreport 1.31.3

• Fix error in example when using 'head' after pipe

DEGreport 1.27.1

• Fix: Export n() from dplyrs.[#27](https://github.com/lpantano/DEGreport/issues/27#issuecomment-819201968)

DEGreport 1.25.3

• Feature: degPlot accepts sizePoint as parameter to indicate the size of the plotted points.

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

DEGreport 1.25.1

• Feature: degPlot will keep the gene order given by the user.

DEGreport 1.23.3

• Fix: pass min_counts parameter to degPlotCluster

DEGreport 1.23.2

• Fix: adopt class(counts)[1] to check classes

DEGreport 1.23.1

• Feature: add prefix to clusters plot in 'degPlotCluster'

DEGreport 1.21.2

• Feature: add 'scale' option to degSignature
• Feature: add lfdr support from fdrtools to degCombs and DEGSet object.

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.

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.

DEGreport 1.19.1

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

DEGreport 1.17.8

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

DEGreport 1.17.7

• Fix: re-format NEWS file

DEGreport 1.17.6

• Fix: Error in degCovariate when no correlation exists.

DEGreport 1.17.5

• Fix: Fix documentation warning.

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.

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.

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.

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

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.

DEGreport 1.15.1

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

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.

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.

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.

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

DEGreport 1.13.6

• Feature: Add degPCA plot from Rory Kirchner

DEGreport 1.13.5

• Feature: Accept matrix for degWidePlot

DEGreport 1.13.4

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

DEGreport 1.13.3

• Feature: Add degMDS for PCA like clustering figures
• Feature: Add labels parameters to degPlot

DEGreport 1.13.2

• Feature: add degFilter to filter genes by group

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

DEGreport 1.11.7

• Fix: Add new contributor

DEGreport 1.11.6

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

DEGreport 1.11.4

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

DEGreport 1.11.3

• Fix: * Fix order of clusters figures that are not in the correct place in some cases with many groups.

DEGreport 1.11.2

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

DEGreport 1.11.1

• Fixes: print clusterProfiler output.

DEGreport 1.9.9

• Fixes: * Fix the reduccion of clusters to use correlation values directly.
• Fixes: GO enrichment function. Input genes was wrong.

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.

DEGreport 1.4.0

• Fix SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG

DEGreport 1.01.01

• Fix BUG WHEN ONLY ONE GENE IS DEG

DEGreport 0.99.12

• CORRECT DOC OF createReport

DEGreport 0.99.11

• ADD ncores TO REPORT CREATION

DEGreport 0.99.10

• REMOVE BIOMART FROM VIGNETTES DUE TO WINDOWS UNKNOWN BUILD ISSUES

DEGreport 0.99.9

• ADDING PARALLELIZATION TO BAYESIAN INFERENCE

DEGreport 0.99.4

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