← Back to Atlas Home

🔬 Complete Analysis Pipeline

All computational analyses for "A molecular atlas of human granulopoiesis"

📋 Analysis Workflow:
  1. Data Preparation → Process raw data (RNA-seq, Proteomics, miRNA)
  2. Sample Analysis → Quality control and sample clustering
  3. Differential Expression → Stage-specific features
  4. Trajectory Analysis → WGCNA and timeOmics
  5. Functional Analysis → Enrichment and TF analysis
  6. Visualization → Generate figures

📊 Step 1: Data Preparation

Transcriptome Prep
RNA-seq processing
Proteome Prep
MaxQuant processing
miRNA Prep
Small RNA processing
Annotations
Feature annotations
Dataset Setup
Combined datasets
Molecular Numbers
Quantification

🔍 Step 2: Core Analyses

Sample Analysis
QC and clustering
Differential Expression
Stage comparisons
DEX Preparation
DE setup

🧬 Step 3: Advanced Analyses

WGCNA
Co-expression networks
timeOmics
Trajectory analysis
miRNA Effects
miRNA-mRNA interactions
Enrichment
GO and pathways
TF Analysis
Transcription factors
Cell Composition
Proteome shifts

📈 Step 4: Visualization

Trajectory Plots
Caterpillar plots
Multi-Omics Lines
Integrated visualizations

🛠️ Helper Functions

SCN MOA Functions
Custom R functions used throughout analyses
💻 Running the Analysis
  1. Download the processed data
  2. Clone the analysis repository (coming soon)
  3. Install R dependencies: tidyverse, mixOmics, limma, WGCNA, timeOmics
  4. Run scripts in order shown above
📦 Required R Packages
install.packages(c("tidyverse", "pheatmap", "ggrepel", "viridis"))
BiocManager::install(c("limma", "mixOmics", "timeOmics", "WGCNA"))
Back to Atlas Home Download Data View Figures