Batch process genome experiments
batch-analysisskillsetup L2★35
ammawla/encode-toolkit ↗What it does
Batch analyze and compare ENCODE experiments
Best for
Quality screening and comparison across 5+ ENCODE experiments simultaneously.
Inputs
- · ENCODE accessions (5+)
- · Assay/target filter
- · QC threshold dict
Outputs
- · Experiment table
- · Quality tier classification
- · Report markdown
Requires
- · ENCODE API
- · pandas
Preconditions
- · Valid accessions
- · 5+ experiments
- · Consistent assembly
Failure modes
- · Mixed assemblies
- · ERROR audits
- · Batch effects
Trust signals
- · Hitz et al. 2023
- · Landt et al. 2012 QC metrics