diff --git a/docs/content/News.rst b/docs/content/News.rst index 1f37e4627..b60793182 100644 --- a/docs/content/News.rst +++ b/docs/content/News.rst @@ -7,11 +7,22 @@ snakePipes 1.1.0 **26.11.18** * A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were updated. - * RaceID can be skipped in the scRNA-seq workflow. * An optional email can be sent upon pipeline completion. * The RNA-seq pipeline can now produce a fuller report upon completion if you are performing differential expression. * Sample merging in HiC works properly. * GTF files are now handled more generically, which means that they no longer need to have "_gencode" and "_ensembl" in their path. + * WGBS: + * Merging data from WGBS replicates is now an independent step so that dependent rules don't have to wait for successful completion of single CpG stats but can go ahead instead. + * Filtering of differential methylation test results is now subject to two user-modifiable parameters minAbsDiff (default 0.2) and FDR (0.02) stored in defaults.yaml. + * Metilene commandline parameters are now available in defaults.yaml. Defaults are used apart from requesting output intervals with any methylation difference (minMethDiff 0). + * Additional diagnostic plots are generated - p value distribution before and after BH adjustment as well as a volcano plot. + * Automatic reports are generated in every folder containing results of statistical analysis (single CpG stats, metilene DMR stats, user interval aggregate stats), as long as sample sheet is provided. + * R sessionInfo() is now printed at the end of the statistical analysis. + * scRNAseq: + * An extention to the pipeline now takes the processed csv file from Results folder as input and runs cell filtering with a range of total transcript thresholds using monocle and subsequently runs clustering, produces tsne visualizations, calculates top 2 and top10 markers per cluster and produces heatmap visualizations for these using monocle/seurat. If the skipRaceID flag is set to False (default), all of the above are also executed using RaceID. + * Stats reports were implemented for RaceID and Monocle/Seurat so that folders Filtered_cells_RaceID and Filtered_cells_monocle now contain a Stats_report.html. + * User can select a metric to maximize during cell filtering (cell_filter_metric, default: gene_universe). + * For calculating median GPC, RaceID counts are multiplied by the TPC threshold applied (similar to 'downscaling' in RaceID2). snakePipes 1.0.0 (king cobra) released --------------------------------------