Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm

All single cell sequencing datasets, R scripts and installation instructions.

The following instructions allows you to download R and Rstudio to view any gene expression from the single cell datasets.

Download R:

Visit the Comprehensive R Archive Network (CRAN) website, the official source for R: https://cran.r-project.org/.
Choose a CRAN mirror location near you. Select the mirror that's geographically closest to your location for faster download speeds.
Click on the appropriate link for your operating system (Windows, macOS, or Linux).
Follow the installation instructions for your specific operating system. Typically, this involves downloading the installer and running it.
Install R:

Run the downloaded installer.
Follow the on-screen instructions, including choosing installation options if prompted.
Once the installation is complete, you will have R installed on your computer.
Download RStudio:

Visit the RStudio download page: https://www.rstudio.com/products/rstudio/download/.
Scroll down to the "RStudio Desktop" section.
Click on the appropriate link for your operating system (Windows, macOS, or Linux).
Download the installer for RStudio Desktop.
Install RStudio:

Run the downloaded RStudio installer.
Follow the on-screen instructions to complete the installation.
Once you've completed these steps, you'll have both R and RStudio installed on your computer. You can then launch RStudio, and it will automatically detect your R installation and provide an integrated development environment for working with R. You are then able to open up of the four R markdown files (.Rmd) and load in the datasets from the Rds_object folders in order to view the datasets.

Descriptions on the R scripts and Rds objects uploaded below:
Three folders containing R codes and the input to the codes as Rds object format. Navigate into the folder and open the rmd or r script files with R studio and follow the instruction inside to run codes. All script should be able to run with minor edit to the data path customed to each user. All scripts inside each folders should be able to run without requiring the outputs of other scripts. To visualize gene expression of single cell seq dataset as shown in the paper, use folder "1. UMAP_Gene_Viewer". To reproduce the UMAP and sequencing results from annotated matrix files, use folder "2. UMAP, differential analysis and cell trajectory pipeline". To integrate multiple datasets, use folder 3.

所有单细胞测序数据集、R 脚本及安装说明。

以下指南将指导您下载 R 和 RStudio，以便浏览单细胞数据集中的任何基因表达。

下载 R:

访问综合 R 软件包网络（CRAN）官网：https://cran.r-project.org/，这是 R 的官方资源。

选择地理位置上与您最近的 CRAN 镜像位置，以便获得更快的下载速度。

点击适用于您操作系统的相应链接（Windows、macOS 或 Linux）。

遵循针对您特定操作系统的安装说明。通常，这包括下载安装程序并运行它。

安装 R:

运行下载的安装程序。

按照屏幕上的说明操作，包括在需要时选择安装选项。

一旦安装完成，R 将已安装在您的计算机上。

下载 RStudio:

访问 RStudio 下载页面：https://www.rstudio.com/products/rstudio/download/。

滚动至“RStudio Desktop”部分。

点击适用于您操作系统的相应链接（Windows、macOS 或 Linux）。

下载 RStudio Desktop 的安装程序。

安装 RStudio:

运行下载的 RStudio 安装程序。

按照屏幕上的说明完成安装。

完成这些步骤后，您将在计算机上安装 R 和 RStudio。然后，您可以启动 RStudio，它将自动检测您的 R 安装，并提供一个集成的开发环境，以便使用 R 进行工作。之后，您即可打开四个 R Markdown 文件（.Rmd），并从 Rds_object 文件夹中加载数据集以查看数据集。

下述 R 脚本和 Rds 对象的描述：

包含 R 代码及其输入的 Rds 对象格式的三个文件夹。进入文件夹，使用 RStudio 打开 rmd 或 r 脚本文件，并按照其中的说明运行代码。所有脚本在经过对数据路径的少量编辑后均能运行。每个文件夹内的所有脚本均能独立运行，无需依赖其他脚本的输出。为了可视化单细胞测序数据集的基因表达，如图所示，请使用“1. UMAP_Gene_Viewer”文件夹。为了再现从注释矩阵文件中得到的 UMAP 和测序结果，请使用“2. UMAP、差异分析和细胞轨迹管道”文件夹。为了整合多个数据集，请使用第三个文件夹。