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NEWS
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DEGreport News
CHANGES IN DEGreport 1.39.5
* 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