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  • Experience
  • Meet the Team
  • Blog
    • 2026 joint Summer Intern
    • 2026 Summer Intern in Li Lab
  • Courses
    • Hugo Blox
      • Getting Started
      • Guide
        • Project Structure
        • Configuration
        • Formatting
          • Embed Media
          • Buttons
          • Callouts
          • Cards
          • Spoilers
          • Steps
      • Reference
        • Customization
        • Internationalization (i18n)
  • Software
    • Cumulus
    • Pegasus
    • Harmony-Pytorch
    • Cirrocumulus
    • NMF-Torch
    • PROBer
    • DETONATE
    • CSEM
    • RSEM
  • Slides
    • Example Talk: Recent Work
  • Publications
    • Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells
    • Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq
    • A Single-Cell and Single-Nucleus RNA-Seq Toolbox for Fresh and Frozen Human Tumors
    • Thousands of Novel Unannotated Proteins Expand the MHC I Immunopeptidome in Cancer
    • Linking Indirect Effects of Cytomegalovirus in Transplantation to Modulation of Monocyte Innate Immune Function
    • Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
    • Accuracy Assessment of Fusion Transcript Detection via Read-Mapping and De Novo Fusion Transcript Assembly-based Methods
    • Decoding Human Fetal Liver Haematopoiesis
    • Nuclei Multiplexing with Barcoded Antibodies for Single-Nucleus Genomics
    • An example preprint / working paper
    • PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays
    • STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
    • Metrics for Rapid Quality Control in RNA Structure Probing Experiments
    • Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
    • An example journal article
    • Evaluation of de novo Transcriptome Assemblies from RNA-Seq Data
    • De novo Transcript Sequence Reconstruction from RNA-seq using the Trinity Platform for Reference Generation and Analysis
    • An example conference paper
    • RSEM: Accurate Transcript Quantification from RNA-Seq Data with or without a Reference Genome
    • Discoevering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
    • RNA-Seq Gene Expression Estimation with Read Mapping Uncertainty
  • Hugo Blox
    • Getting Started
    • Guide
      • Project Structure
      • Configuration
      • Formatting
        • Embed Media
        • Buttons
        • Callouts
        • Cards
        • Spoilers
        • Steps
    • Reference
      • Customization
      • Internationalization (i18n)
Courses
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Guide

Formatting Project Structure Configuration
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Last updated on Oct 24, 2023

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