+
+
+**I**ntelligent **C**linl**A**bomics **R**esearch **E**xpedition
+
+A modular R framework that takes clinical / omics data all the way from
+raw table to publication-ready figures: statistics and missing-data
+handling, feature selection, machine-learning benchmarking, unsupervised
+subtyping (K-means, NMF, latent profile analysis), and prognostic /
+survival modeling — each with an interactive Shiny deployment layer.
+
+[](https://www.gnu.org/licenses/gpl-3.0)
+
+
+
+**Maintainer:** Huaichao Luo (luohc@uestc.edu.cn) —
+[Google Scholar](https://scholar.google.com/citations?user=XNKOGaIAAAAJ) |
+[ResearchGate](https://www.researchgate.net/profile/Huaichao-Luo) |
+[Lab Twitter/X](https://x.com/Luo_lab)
+
+**Contributor:** Guangchuang Yu — [Lab website (yulab-smu.top)](https://yulab-smu.top)
+
+---
+
+## Contents
+
+- [Overview](#overview)
+- [Installation](#installation)
+- [The four modules](#the-four-modules)
+- [Essential Commands](#essential-commands)
+ - [Module 1 — Data cleaning (`Stat`)](#module-1--data-cleaning-stat)
+ - [Module 2 — Modeling (`Train_Model`)](#module-2--modeling-train_model)
+ - [Module 3 — Subtyping (`Subtyping`)](#module-3--subtyping-subtyping)
+ - [Module 4 — Survival / Prognosis (`PrognosiX`)](#module-4--survival--prognosis-prognosix)
+- [Quick start](#quick-start)
+- [Getting help](#getting-help)
+- [Citation](#citation)
+- [License](#license)
+
+---
+
+## Overview
+
+icare organizes an analysis as a pipeline of **S4 objects**, one per stage,
+each produced by converting the previous one with `ConvertObject()`:
+
+```
+raw data.frame
+ │ CreateStatObject()
+ ▼
+ Stat object ──────────────► baseline table, group comparisons, DEG
+ │ ConvertObject(to = "Train_Model") ConvertObject(to = "Subtyping") Stat_to_PrognosiX()
+ ▼ ▼ ▼
+Train_Model object Subtyping object PrognosiX object
+(classification / (K-means / NMF / LPA) (Cox / RSF / mlr3proba
+ regression, caret) survival learners)
+ │ │ │
+ ▼ ▼ ▼
+ ModelDeployment() New_Sub_Manager() New_Prog_Manager()
+ │ │ │
+ ▼ ▼ ▼
+deploy_clinlab_app() launch_sub_deploy_app() launch_prog_deploy_app()
+```
+
+Every stage keeps a record of what was done to the data (imputation
+values, scaling parameters, selected features, trained models) inside the
+object itself, so the *exact same* transformation can be replayed on new
+patients at prediction time.
+
+## Installation
+
+```r
+# install.packages("remotes")
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