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A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction

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For Complete Instructions on useage, visit: GEMmaker documentation

GEMmaker is a Nextflow workflow for large-scale gene expression sample processing, expression-level quantification and Gene Expression Matrix (GEM) construction. Results from GEMmaker are useful for differential gene expression (DGE) and gene co-expression network (GCN) analyses. The GEMmaker workflow currently supports Illumina RNA-seq datasets.

GEMmaker is:

Easy to Use

Ease of Use

  • No bioinformatics software installation required
  • Runs on a stand-alone computer or High Performance Compute (HPC) cluster
  • Simple configuration file setup
  • Resulting data is ready for Differential Gene Expression (DGE) or Gene Co-Expression Network (GCN) analysis
  • Full online documentation

Reproducible

Reproducible

  • Software versions and computing environment are the same every time an experiment is repeated
  • Sharing input data and config files ensures anyone can reproduce exact results

Interoperable

Interoperable

  • Uses a variety of bioinformatics tools
  • Integrates with iRODs for easy data movement
  • Easily retrieves samples from NCBI’s Sequence Read Archive (SRA)
  • Can combine local samples with those from SRA
  • Runs on many modern HPC systems

Discoverable

Findable

  • Sample metadata is retrieved from NCBI SRA
  • Controlled vocabularies are used to automatically remap SRA annotations
  • JSON-format metadata files are created for each sample
  • Metadata files can be integrated with data in iRODs for querying

Scalable

Scalable

  • Useful for small DGE projects with 100s of samples as well as large GCN projects with 1000s of samples
  • Cleans up intermediate files once they are no longer needed
  • Keeps storage requirements to a minimum

Tools

GEMmaker uses the following tools:

Usage

For Complete Instructions on useage, visit: GEMmaker documentation

Acknowledgments

GEMmaker is a collaborative project of the Ficklin and Feltus programs at Washington State University and Clemson University respectively with guidance from RENCI.

GEMmaker is funded by the NSF SciDAS project, award #1659300

"WSU"   "Clemson"   "RENCI"   "NSF"   "SciDAS"

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A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction

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