2. scVMAP usage

Below, we will explain how to use the scVMAP (https://bio.liclab.net/scvmap/) platform based on the different functional levels on the navigation bar.

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The detailed manual is as follows:

• 2.1 Home
  • 2.1.1 Trait or disease search
  • 2.1.2 Single cell sample search
  • 2.1.3 Gene search
  • 2.1.4 TF search
  • 2.1.5 Variant search
• 2.2 Data-browse
  • 2.2.1 Single cell chromatin accessibility data
    • 2.2.1.1 Granularity: Sample ID
    • 2.2.1.2 Granularity: Cell type
  • 2.2.2 Trait or disease data
    • 2.2.2.1 FINEMAP
    • 2.2.2.2 SuSiE
• 2.3 Search
  • 2.3.1 Search information by category or source cohort
    • 2.3.1.1 Category
    • 2.3.1.2 Source cohort
  • 2.3.2 Search information by tissue type or cell type
    • 2.3.2.1 Tissue type
    • 2.3.2.2 Cell type
  • 2.3.3 Search information by gene
  • 2.3.4 Search information by TF
  • 2.3.5 Search information by SNP
• 2.4 Detail
  • 2.4.1 Overview
    • 2.4.1.1 scATAC-seq
    • 2.4.1.2 Fine-mapping result
  • 2.4.2 TRS
    • 2.4.1.1 The first part
    • 2.4.1.2 The second part
  • 2.4.3 Differential genes
  • 2.4.4 Trait-relevant genes
  • 2.4.5 Gene hub network
  • 2.4.6 Differential TFs
  • 2.4.7 Trait-relevant TFs
  • 2.4.8 TF hub network
  • 2.4.9 Integrated network
• 2.5 Analysis
  • 2.5.1 Analyzing variant-to-function mapping
  • 2.5.2 Analyzing variant-to-function mapping with genes
  • 2.5.2 Analyzing variant-to-function mapping with TFs
  • 2.5.4 Comparative analysis between samples or traits
• 2.6 Statistics
  • 2.6.1 Visualization
  • 2.6.2 Display
• 2.7 Download
  • 2.7.1 Download TRS data for each sample
    • 2.7.1.1 Overview of scATAC-seq data: txt file
    • 2.7.1.2 scATAC-seq data: H5AD file
    • 2.7.1.3 The result data of method g-ChromVAR: H5AD file
    • 2.7.1.4 The result data of method SCAVENGE: H5AD file
  • 2.7.2 Download fine-mapping result data for each sample
    • 2.7.2.1 Overview of fine-mapping result data: xlsx file
    • 2.7.2.2 Fine-mapping result data
  • 2.7.3 Download other data
    • 2.7.3.1 Fine-mapping result data: tar.gz file
    • 2.7.3.2 Differential gene data: txt file
    • 2.7.3.3 Differential TF data: txt file
    • 2.7.3.4 MAGMA result data: tar.gz file
      • 2.7.3.4.1 Annotation: txt file (After decompression)
      • 2.7.3.4.1 Gene analysis -raw data: txt file (After decompression)
    • 2.7.3.5 HOMER result data: tar.gz file
    • 2.7.3.6 Gene enrichment analysis results: tar.gz file
      • 2.7.3.6.1 Gene enrichment for differential genes
      • 2.7.3.6.2 Gene enrichment results of traits (hg19/hg38)
    • 2.7.3.7 Gene regulation/V2G annotation data:
      • 2.7.3.7.1 Common SNP: txt file (After decompression)
      • 2.7.3.7.2 eQTL: txt file (After decompression)
      • 2.7.3.7.3 Risk SNP: txt file (After decompression)
      • 2.7.3.7.4 Enhancer (SEA v3): txt file (After decompression)
      • 2.7.3.7.5 Enhancer (SEdb v2): txt file (After decompression)
      • 2.7.3.7.6 Super enhancer (dbSUPER): txt file (After decompression)
      • 2.7.3.7.7 Super enhancer (SEA v3): txt file (After decompression)
      • 2.7.3.7.8 Super enhancer (SEdb v2): txt file (After decompression)
      • 2.7.3.7.9 3D chromatin interaction: bed file (After decompression)
      • 2.7.3.7.10 MPRA: csv file
• 2.8 Contact
• 2.9 On-line analysis