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NEWS
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NEWS
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CHANGES IN VERSION 1.6.3
------------------------
o now allows fitType="mean" in DESeq2
CHANGES IN VERSION 1.6.2
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o fixed a bug in template_script_edgeR_CL.r to use forceCairoGraph option
o fixed a bug in loadCountData() function
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o new boolean parameter forceCairoGraph
o adapt size of PNG plots if width/height are too large
CHANGES IN VERSION 1.6.0
------------------------
o use "percentage" instead of "proportion" in some plots
o added pandoc-citeproc as potential requirement for some users
o added rmarkdown version 1.4 requirement to have knit_root_dir parameter in render()
o use file.path() instead of paste() when dealing with paths to import/create files
o added cpmCutoff parameter to writeReport.edgeR()
CHANGES IN VERSION 1.5.1
------------------------
o fixed a bug in bullet points
CHANGES IN VERSION 1.5.0
------------------------
o new HTML report (dynamic table of contents, automatic bibliography)
o simplified SERE calculations
o use of warning() instead of print() in checkParameters.edgeR() and checkParameters.DESeq2()
CHANGES IN VERSION 1.4.1
------------------------
o SARTools now accepts count files generated by featureCounts (still one count file per sample)
o added sample names and colors to the diagnostic of the size factors with DESeq2
CHANGES IN VERSION 1.4.0
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o added a parameter in exportResults.DESeq2() and exportResults.edgeR() to avoid exporting the results
o adapted the plots when studying many samples and performing many comparisons
o now check if there are some NA in the target file
o now check if some counts are not integers (as required by edgeR and DESeq2)
o added the command line scripts to the repository (need to run SARTools with Galaxy)
CHANGES IN VERSION 1.3.2
------------------------
o pairwiseScatterPlots() function not executed with more than 30 samples
CHANGES IN VERSION 1.3.1
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o Increased plot resolution to 300ppi
o New instructions to install SARTools with Conda
o Update of the citation of SARTools (PLoS One 2016)
CHANGES IN VERSION 1.3.0
------------------------
o Adapted the package to the new Bioconductor release (April 2016)
o Fixed a bug when using the Bonferroni correction with edgeR
CHANGES IN VERSION 1.2.0
------------------------
o Improved the sessionInfo() printing in the HTML reports
o Improved the README and the vignette
o Figure size now depends on the number of samples (in some cases)
o Fixed a bug when selecting the most variant features in PCAPlot()
o Fixed a bug when setting cpmCutoff to 0 using the edgeR script
o Vignette name is now "SARTools" instead of "tutorial"
o Mofidied the way of getting the independent filtering threshold (bug due to new DESeq2 version)
o New versions of R (3.2.2), DESeq2 (1.10.0) and edgeR (3.12.0) required
CHANGES IN VERSION 1.1.0
------------------------
o Improved the installation guidelines from GitHub
o Vignette now in Markdown for a better integration in GitHub
o Added the normalizationMethod parameter to the edgeR pipeline to allow for a RLE or upperquartile normalization
CHANGES IN VERSION 1.0.4
------------------------
o Order counts according to features names in loadCountData()
o Small modifications in the DESeq2 report due to the changes in version 1.0.3
CHANGES IN VERSION 1.0.3
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o If use of DESeq2, the cooksCutoff parameter is now TRUE or FALSE (instead of NULL, Inf or a numeric)
CHANGES IN VERSION 1.0.2
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o Added volcano plots to the HTML reports
CHANGES IN VERSION 1.0.0
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o First version publicly available on GitHub
CHANGES IN VERSION 0.99.6
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o Added batch argument to loadTargetFile()
o Simplified the R script templates with wrappers
CHANGES IN VERSION 0.99.5
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o Now check the format/validity of the parameters at the beginning of the script
o Added functions checkParameters.DESeq2() and checkParameters.edgeR()
o Added small precisions in the vignette
CHANGES IN VERSION 0.99.4
-------------------------
o First version of the package