@@ -24,11 +24,11 @@ However the framework can be applied to any other context (see the `pipeComp_dea

 `pipeComp` is especially suited to the benchmarking of pipelines that include many steps/parameters, enabling the exploration of combinations of parameters and of the robustness of methods to various changes in other parts of a pipeline. It is also particularly suited to benchmarks across multiple datasets. It is entirely based on _R_/Bioconductor, meaning that methods outside of _R_ need to be called via _R_ wrappers. `pipeComp` handles multithreading in a way that minimizes re-computation and duplicated memory usage, and computes evaluation metrics on the fly to avoid saving many potentially large intermediate files, making it well-suited for benchmarks involving large datasets.

-This readme gives a very brief overview of the package. For more detailed information on the framework, refer to the [pipeComp vignette](vignettes/pipeComp.Rmd). For information specifically about the scRNAseq pipeline and evaluation metrics (as well as more complex examples usages of the plotting functions), see the [pipeComp_scRNA vignette](vignettes/pipeComp_scRNA.Rmd). For a completely different example, with walkthrough the creating of a new `PipelineDefinition`, see the [pipeComp_dea vignette](vignettes/pipeComp_dea.Rmd).

+This readme gives a very brief overview of the package. For more detailed information on the framework, refer to the [pipeComp vignette](http://bioconductor.org/packages/devel/bioc/vignettes/pipeComp/inst/doc/pipeComp.html). For information specifically about the scRNAseq pipeline and evaluation metrics (as well as more complex examples usages of the plotting functions), see the [pipeComp_scRNA vignette](http://bioconductor.org/packages/devel/bioc/vignettes/pipeComp/inst/doc/pipeComp_scRNA.html). For a completely different example, with walkthrough the creating of a new `PipelineDefinition`, see the [pipeComp_dea vignette](http://bioconductor.org/packages/devel/bioc/vignettes/pipeComp/inst/doc/pipeComp_dea.html).

 ### Recent changes

-* In `pipeComp` 0.99.43, there is now the possibility to continue runs despite errors (see the `skipErrors` argument of `runPipeline`, and the 'Handling errors' section of the [pipeComp vignette](vignettes/pipeComp.Rmd).).

+* In `pipeComp` 0.99.43, there is now the possibility to continue runs despite errors (see the `skipErrors` argument of `runPipeline`, and the 'Handling errors' section of the [pipeComp vignette](http://bioconductor.org/packages/devel/bioc/vignettes/pipeComp/inst/doc/pipeComp.html).).

 * In `pipeComp` 0.99.26 on, the plotting functions for the scRNAseq clustering pipeline (`scrna_evalPlot_DR` and `scrna_evalPlot_clust`) have been replaced by more flexible, pipeline-generic functions (`evalHeatmap`) and a silhouette-specific plotting function (`scrna_evalPlot_silh`). The general heatmap coloring scheme has also been changed to make meaningful changes clearer.