CHANGES IN VERSION 1.18.2 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Renamed load_install() as load_check() as this function now only checks that the package(s) was installed and returns an error if missing. The error shows the user how to install the package(s) they are missing instead of installing them automatically. This complies with Marcel Ramos' request at https://github.com/leekgroup/recount/issues/14. CHANGES IN VERSION 1.17.2 ------------------------- NEW FEATURES o Add ORCID's following changes at http://bioconductor.org/developers/package-guidelines/#description 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