Monocle 2.0.0系列新闻= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 2.6.1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - o knn-based密度峰值集群不是一般的数据集。回滚到之前的densityPeak聚类算法,将其设置为默认的算法。新鲁汶处理大型数据集的聚类算法(> 50 k细胞)。o为importCDS几个bug修复,exportCDS功能。版本2.6.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - o官方发布的特性在2.5.0 2.5.0 BioC版本- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - o各种情节工具可视化复杂的发展轨迹(plot_complex_cell_trajectory),多路动力学曲线和多路的热图(plot_multiple_branches_pseudotime plot_multiple_branches_heatmap)。o ClusterCells现在原则上支持集群为100 k +细胞取决于过程的峰值密度聚类算法为基础的资讯。densityClust包0.3版本需要用户使用此功能。o新功能支持导入走开或修cd到单片眼镜,反之亦然(importCDS exportCDS)。版本测试盒框- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - o默认expressionFamily现在negbinomial。大小,而不是托比特书。如果您使用的是TPM或FPKM数据,我们敦促你将它与relative2abs相对记录数量和使用CellDataSet对象的负二项分布。 o Revamped clusterCells functionality based on t-SNE and densityPeak o New procedure for selected ordering genes called "dpFeature". See vignette for details. Version 2.1.1 -------------------------------------------------------------------------------- BUGFIXES o Fixed an problem where reduceDimension would return different results on repeated runs given the same inputs.The problem was actually in DDRTree in two places: kmeans and irlba. We now call irlba with deterministically initialized eigenvectors and kmeans with deterministically selected rows of the input. o Fixed a problem in classifyCells related to joining factors and levels. This would generate annoying warnings. o Fixed the check for valid sizeFactors prior to differentialGeneTest. Without this check, differentialGeneTest would report FAIL on all genes because of factors not having enough levels. Version 2.1.0 -------------------------------------------------------------------------------- FEATURES o Monocle's algorithm for converting relative expression values (e.g. TPMs) into absolute transcript counts, called "Census" has been re-designed. The new version is much more accurate. Census is available through the relative2abs() function. The interface to this function has changed, and the output values will be quite different from the old version. The main change is that the version in 1.99.0 reported cDNA counts, as estimated in each cell's cDNA library. Now, relative2abs reports estimates of mRNA counts in the lysate. These are easier to compare with experiments that estimate mRNA counts via the use of spike-in controls. o A new heatmap function plot_pseudotime_heatmap() replaces the old plot_genes_heatmap(). o Lots of new documentation. More to follow in upcoming releases. BUGFIXES o Ordering cells with DDRTree no longer compresses cells at the tips of trajectories. o Pseudo counts are now applied correctly no matter what the underlying distribution used to model expression is. o Variance stabilization is applied correctly when a CellDataSet object's expressionFamily is negbinomial.size(). o The gene_id field in results from calculateMarkerSpecificity is now a character instead of a factor. This was leading to indexing errors and nonsensical semi-supervised clustering and ordering results. o BEAM() and plot_branched_heatmap() now use cBind instead of cbind, fixing an issue with sparse matrices. Version 1.99.0 -------------------------------------------------------------------------------- o The first public release of the Monocle 2 series. For a summary of new features and changes, please see: http://cole-trapnell-lab.github.io/monocle-release/features/ CHANGES in monocle 1.1.5: * After grappling with Bioconductor build issues in HSMMSingleCell related to VGAM updates, we have moved to a different data layout in HSMMSingleCell, which has caused some changes in the vignette. CHANGES in monocle 1.1.1: * Fixed a bug in responseMatrix() that occurs when you don't have any genes that fail VGAM fitting