【slingshot】trajectory inference

condiments Paper • condimentsPaper

First example: TGF-beta dataset • bioc2021trajectories

slingshot requires a minimum of two inputs: (1)a matrix representing the cells in a reduced-dimensional space. (2)a vector of cluster labels.

主要步骤：

（1）getLineages function to identify global lineage structrue by construsting MST on the clusters

（2）getCurves function to construct smooth curves and infer the psudotime variable

simulated dataset 1 (single trajectory) and dataset 2 (bifurcating)

#####dataset1
# generate synthetic count data representing a single lineage
means <- rbind(# non-DE genesmatrix(rep(rep(c(0.1,0.5,1,2,3), each = 300),100),ncol = 300, byrow = TRUE),# early deactivationmatrix(rep(exp(atan( ((300:1)-200)/50 )),50), ncol = 300, byrow = TRUE),# late deactivationmatrix(rep(exp(atan( ((300:1)-100)/50 )),50), ncol = 300, byrow = TRUE),# early activationmatrix(rep(exp(atan( ((1:300)-100)/50 )),50), ncol = 300, byrow = TRUE),# late activationmatrix(rep(exp(atan( ((1:300)-200)/50 )),50), ncol = 300, byrow = TRUE),# transientmatrix(rep(exp(atan( c((1:100)/33, rep(3,100), (100:1)/33) )),50), ncol = 300, byrow = TRUE)
)
counts <- apply(means,2,function(cell_means){total <- rnbinom(1, mu = 7500, size = 4)rmultinom(1, total, cell_means)
})
rownames(counts) <- paste0('G',1:750)
colnames(counts) <- paste0('c',1:300)
sce <- SingleCellExperiment(assays = List(counts = counts))#####dataset2
library(slingshot, quietly = FALSE)
data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cldim(rd) # data representing cells in a reduced dimensional space

【slingshot】trajectory inference相关推荐

【2021-12-22】【Kotlin】Type inference failed. Expected type mismatch: inferred type is HashSet but Set
类似这样的错误提示: Type inference failed. Expected type mismatch: Inferred type is HashSet<String>? bu ...
【全文翻译】Membership Inference Attacks Against Machine Learning Models
针对机器学习模型的成员推理攻击 I. INTRODUCTION II. MACHINE LEARNING BACKGROUND (机器学习背景) III. PRIVACY IN MACHINE LEA ...
【文章思路、算法分析】Membership Inference Attacks Against Machine Learning Models
白菜苗 1.成员推理攻击目的 2.阴影模型构建 3.攻击模型的构造 4.算法分析 5.总结如果你不小心又亦或是专门寻找这篇文献相关知识,那么很高兴能和你们分享这篇文章. 何谓成员推理攻击,陌生而又抽 ...
【slingshot and tradeSeq】differential analysis between different lineages
tradeSeq是同一团队做的R包,主要功能有: (1)比较不同conditions的lineages.例如一组mock stimulation, 一组TGF stimulation,检验两个line ...
【ECCV2020】Spatio-Temporal Graph Transformer Networks for Pedestrian Trajectory Prediction
[ECCV2020]用于行人轨迹预测的时空图 Transformer 网络摘要了解人群运动动力学对于现实世界的应用至关重要,例如监控系统和自动驾驶.这是具有挑战性的,因为它需要对具有社会意识的人群 ...
【总结】为什么对累积奖励减去baseline项能起到减小方差的作用？
深度强化学习实验室论坛:http://deeprlhub.com/ 来源:https://zhuanlan.zhihu.com/p/98506549 作者: 风清云很多论文的工作都专注于减少pol ...
【camera】YOLOV7实现实例分割+目标检测任务（训练、测试、量化、部署）
[camera]YOLOV7实现实例分割+目标检测任务代码下载地址训练.测试.量化.部署代码训练 For training, quite simple, same as detectron2: ...
【FPGA】Buffer专题介绍（二）
目录背景 IBUF IBUFDS IBUFG IBUFGDS 背景这篇博文是下面这篇博文的继续: [FPGA]Buffer专题介绍(一) 但介绍方式我想放的更自由一点,要不然就是官方文档了. IB ...
【FPGA】Buffer专题介绍（一）
目录背景 BUFG BUFGCE BUFGCE_1 BUFGMUX and BUFGMUX_1 BUFGP BUFH BUFIO2 BUFIO2FB 背景在数据手册 Spartan-6 Libra ...

【slingshot】trajectory inference

【slingshot】trajectory inference相关推荐

最新文章

热门文章