A phylogeny-based computational framework that infers the transcriptional states of unobserved internal nodes from cell phylogenies via lineage-specific upregulated genes (LUGs), integrating lineage tracing with scRNA-seq to reconstruct ancestral transcriptomes and build lineage-resolved cell atlases.基于系统发育的计算框架：利用谱系特异性上调基因（LUGs），从细胞系统发育树推断未观测内部节点的转录状态；结合谱系追踪与单细胞 RNA 测序重建祖先转录组，支持构建谱系分辨的细胞图谱。

Interactive in-browser visualization of 30 zebrafish cell lineage trees: nodes are coloured by cell type, with smooth zoom/pan, flexible cell selection and live cell-type composition charts. Live demo: https://shadowdeng1994.github.io/LEAP_web/30 个斑马鱼细胞谱系树的交互式网页可视化：节点按细胞类型着色，支持平滑缩放/平移、多种方式选择细胞，并实时显示所选细胞的类型组成。在线使用：https://shadowdeng1994.github.io/LEAP_web/

Beta version of TarCA (targeting coalescent analysis): estimates the progenitor number (Np) of any defined tissue or cell population from its cell phylogeny via the average coalescent rate at its monophyletic clades, independent of pre-set markers; rewritten for higher computational efficiency.TarCA（靶向溯祖分析）测试版：基于细胞系统发育树估计任意组织或细胞群体的祖细胞数目（Np）——计算目标组织单系进化枝上的平均溯祖速率并取倒数，无需预设标记；为提升计算效率而重写的紧凑实现。

Data and code for the Np dynamic reconstruction in Drosophila melanogaster with SMALT, quantifying the longitudinal dynamics of actively dividing parental cells (Np) during organ development, and informing symmetric vs. asymmetric division balance and a sigmoid organ-growth model.利用 SMALT 对黑腹果蝇进行 Np（活跃分裂的祖先细胞数目）动态重建的数据与代码：刻画各器官发育过程中 Np 的纵向动态，进而揭示细胞分裂的对称/不对称平衡与器官生长的sigmoid 规律。

Data and R scripts for analysing the SARS-CoV-2 mutation signature: comparing public viral genomes to infer the pre-outbreak mutation spectrum, which is 99.9% identical to that of RaTG13, suggesting they shared almost the same host environment before the outbreak.分析 SARS-CoV-2 突变特征的数据与 R 脚本：比较公开病毒基因组，推断病毒在疫情前积累的突变谱，发现其与 RaTG13 的突变谱高达 99.9% 一致，提示二者在疫情前共享几乎相同的宿主环境。

A small R toolbox for free-form vector drawing directly as ggplot2 layers — trace outlines from PNG images, build geometric shapes (circle, ellipse, fan, rounded rectangle, smooth paths), transform coordinates, apply ready-made themes, and compose everything into a single ggplot2 plot.FreeDrawInR 是一个把自由绘制直接变成 ggplot2 图层的 R 工具箱，用于制作示意图、插图和图表：支持从 PNG 图像描摹轮廓、构建圆/椭圆/扇形/圆角矩形/平滑路径等几何形状、平移缩放旋转坐标系、套用现成主题，并拼装成一张完整的 ggplot2 图。

A 3D explainer for ggplot2's gtable/grob structure: it peels a ggplot apart layer by layer to show where each visual element comes from and in what order it is drawn. Pure static HTML/CSS/JS — no backend or CDN; open preview.html directly or host it on GitHub Pages.用 3D 拆解的方式讲解 ggplot2 的 gtable/grob 结构：把一张图拆成一层一层，直观展示每个图层元素由哪里来、按什么顺序叠出来。纯静态（HTML/CSS/JS），没有后端、不依赖 CDN，可直接打开 preview.html 或部署到 GitHub Pages。