CHANGES IN VERSION 1.15.4 ------------------------- BUG FIXES o Fix a bug in the order that was reported and fixed by @bounlu at https://github.com/leekgroup/regionReport/pull/9/ CHANGES IN VERSION 1.15.3 ------------------------- BUG FIXES o Fixed an issue with DESeq2Exploration.Rmd that affected both DESeq2Report and edgeReport. This should also fix the recount bioc-release (3.7) and bioc-devel (3.8) branches. o Fixed a NAMESPACE issue with rmarkdown::html_document and BiocStyle::html_document CHANGES IN VERSION 1.15.2 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Use BiocManager CHANGES IN VERSION 1.15.1 ------------------------- BUG FIXES o Fix namespace issue in relation to BiocStyle::html_document2 CHANGES IN VERSION 1.11.6 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Changed the default style to BiocStyle::html_document to mirror recent changes in BiocStyle. CHANGES IN VERSION 1.11.4 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Vignette now uses the new BiocStyle::html_document that was recently released. CHANGES IN VERSION 1.11.2 ------------------------- BUG FIXES o Fixed the citations. o Fixed DESeq2Report() for limma-results so that it will properly cite limma. CHANGES IN VERSION 1.11.1 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o DESeq2Report() can now be used with other software if their results are made to look like DESeq2 results. For example, with limma-voom results. BUG FIXES o Made the DESeq2Report() more robust in case rlog() fails initially. CHANGES IN VERSION 1.9.1 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Changed the default style to BiocStyle::html_document2. CHANGES IN VERSION 1.7.10 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Help pages now document advanced arguments. CHANGES IN VERSION 1.7.2 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Dropped defunct functions. CHANGES IN VERSION 1.5.48 ------------------------- BUG FIXES o Fixed a bug in derfinderReport() for a case when there are significant regions but not all regions have finite areas. CHANGES IN VERSION 1.5.43 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o edgeReport() now includes two edgeR specific plots: one showing the BCV and another showing a 2-dim MDS. Also added more edgeR citations that I missed earlier: thank you Gordon Smyth! CHANGES IN VERSION 1.5.33 ------------------------- NEW FEATURES o Added the function edgeReport() for creating HTML or PDF reports based on edgeR results. Together with DESeq2Report() now regionReport supports the two most used packages for RNA-seq feature-level analysis. CHANGES IN VERSION 1.5.19 ------------------------- NEW FEATURES o Added the templates 'templatePvalueHistogram' and 'templateHistogram' to be used with renderReport() if you prefer histogram plots instead of density plots. CHANGES IN VERSION 1.5.12 ------------------------- NEW FEATURES o Added the function DESeq2Report() for creating HTML or PDF reports based on DESeq2 results. This should also be useful to explore derfinder results created from the expressed regions-level approach. SIGNIFICANT USER-VISIBLE CHANGES o Added a 'digits' argument to control how to round some numerical variables in all type of reports. o Added a 'theme' argument to allow setting the ggplot2 theme for the plots. BUG FIXES o Improved the PDF versions of all reports by hiding code and shortening tables. Also added a warning to switch the device to 'pdf' for PDF output since it looks better than the default 'png'. CHANGES IN VERSION 1.5.6 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Switched to using rmarkdown instead of knitrBootstrap as the default engine for creating the reports. CHANGES IN VERSION 1.3.8 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o renderReport() and derfinderReport() now show Manhattan plots for p-value variables (p-value, q-value, FWER adjusted p-value). CHANGES IN VERSION 1.3.7 ------------------------ NEW FEATURES o renderReport() now has the 'densityTemplates' argument via which users can customize the density plots for the p-value variables and the continuous variables. This addresses one of David Robinson's requests at http://f1000research.com/articles/4-105/v1 CHANGES IN VERSION 1.3.6 ------------------------ NEW FEATURES o Added a vignette with an example report from bumphunter results. CHANGES IN VERSION 1.3.5 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Merged pull request https://github.com/leekgroup/regionReport/pull/7 o Added "template" argument to renderReport and derfinderReport to customize the knitr template used o Wrapped code that works in a temporary directory in with_wd function, which evaluates in the directory but returns to the original directory in the case of a user interrupt or error (with on.exit) CHANGES IN VERSION 1.3.4 ------------------------ NEW FEATURES o Reports now have a link to the BibTeX file used for the references. This addresses http://f1000research.com/articles/4-105/v1#reflist Karthik Ram's bullet point number 4. CHANGES IN VERSION 1.3.3 ------------------------ NEW FEATURES o Now uses derfinderPlot::vennRegions() to show venn diagram of genomic states. Requires derfinderPlot version 1.3.2 or greater. o derfinderReport() now has a 'significantVar' argument that allows users to choose between determining significant regions by P-values, FDR adjusted P-values, or FWER adjusted P-values (if FWER adjusted P-values are absent, then FDR adjusted P-values are used instead, with a warning). CHANGES IN VERSION 1.3.2 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Deprecated functions with underscores in their names in favor of camelCase functions. This was done to simplify the package. CHANGES IN VERSION 1.3.1 ------------------------ BUG FIXES o Fixed renderReport() and derfinderReport() so they'll open the correct URL when interactive() == TRUE and the user has knitrBootstrap version 0.9.0 installed instead of the latest GitHub version. CHANGES IN VERSION 1.1.9 ------------------------ NEW FEATURES o Introduced renderReport() which creates a simple exploratory report for any set of genomic regions. It allows the user to further customize the report by using a child file. o You can now use the 'output_format' advanced parameter on both renderReport() and derfinderReport() to output a PDF file instead of an HTML file. The interactive tables are lost and only the top 20 rows are shown. CHANGES IN VERSION 1.1.8 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Adapted to work with bumphunter >= 1.7.6 CHANGES IN VERSION 1.1.7 ------------------------ NEW FEATURES o Users can now control 'output_format' and 'clean' options from rmarkdown::render() when running derfinderReport() CHANGES IN VERSION 1.1.3 ------------------------ BUG FIXES o Adapted derfinderReport() to derfinder 1.1.5 CHANGES IN VERSION 0.99.0 ------------------------- NEW FEATURES o Preparing to submit to Bioconductor. SIGNIFICANT USER-VISIBLE CHANGES o Updated the vignette and the package to work with recent versions of the packages this package depends on. o Renamed the package from derfinderReport to regionReport and generateReport() to derfinderReport(). In the future we will add another report for a general GRanges object. o Simplified derfinderReport()'s call by using advanced arguments. o Added Travis integration. CHANGES IN VERSION 0.0.18 ------------------------- o Now derfinderReport() has a 'chrsStyle' argument to match changes in derfinder version 0.0.60. 'chrsStyle' is set to 'UCSC' by default. CHANGES IN VERSION 0.0.17 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Made more robust for cases where there is a small number of significant DERs: need at least 3 observations by chr for the chr to be included in the density plots. CHANGES IN VERSION 0.0.16 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o MA-style plots now use the scaling factor. o Using a GAM smoother instead of loess for MA-style plots. Helps for cases with many regions. CHANGES IN VERSION 0.0.13 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added a vignette CHANGES IN VERSION 0.0.12 ------------------------- BUG FIXES o complying with BiocCheck version 1.0.0 CHANGES IN VERSION 0.0.11 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o genomicState data moved to derfinder 0.0.53 CHANGES IN VERSION 0.0.8 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Now requires knitrBootstrap 1.0.0 o Matches derfinder version 0.0.49 CHANGES IN VERSION 0.0.3 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Matches derfinder version 0.0.34 CHANGES IN VERSION 0.0.1 ----------------------- NEW FEATURES o Migrated from derfinder