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Welcome to the gEAR upload documentation!

The gene Expression Analysis Resource platform currently supports the upload of:

• Bulk RNASeq data
• Single-Cell Sequencing data
• Microarray data
• Epigenetic data

To assist users with uploading their data, we maintain documentation for uploading data from several different starting formats including programmatically generated files or through Excel. To find the documentation best suited for your upload needs, please see the links below. If you have any questions, or would like assistance with uploading please contact the curator team (Contact us).

Bulk RNAseq data

graph TD;
      A-->B;
      A-->C;
      B-->D;
      C-->D;

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• Preparing bulk RNAseq data using code (slides)
  • Preparing bulk RNAseq data (R code)
  • Preparing RNAseq data from Recount 3 (R code)
• Preparing bulk RNAseq data via Excel (slides)
• Example upload files

Single Cell RNAseq

• Preparing single cell data via code (slides)
  • Preparing single cell data (R code)
• Preparing single cell data via Excel (slides)
• Example files
  • Processed scRNA files
  • Raw scRNA matrix

Microarray data

• Prepare GEO microarray data for upload

Epigenetic data (Epiviz)

• Uploading epigenetic data to gEAR (slides)
  • Preparing BigWig/BigBed files from narrow peak files (R code)