Our GitHub Code Repositories

• Maurano Lab:

  • mapping

  • finetune-enformer (Enformer model fine-tuning code to train on experimentally evaluated synthetic constructs delivered to a genomic loci)

  • soda (Soda plot gallery generator)

  • sge2slurm (Compatibility wrappers for adapting SGE workflows to SLURM)

  • trackhub (create, manage, and upload track hubs for use in the UCSC genome browser)

  • decal (Differential Expression analysis of Clonal Alterations Local effects)

  • hybridmouse

  • UKBB_FINEMAP_targetgene

  • GWAS_plots (Performs enrichment plots of GWAS p-value lists in DHSs)

• Brosh Lab:

  • SnapGene Features to BED File Batch Converter

• Fenyo Lab:

  • L1EM (Estimate locus specific human LINE-1 expression)

  • TIPseqHunter

  • transposcope

  • transposcope_ui

  • simspace (Python framework for simulating spatial omics data with realistic cellular distributions and tissue organization)

• Tan Lab:

  • CANVAS — CANcer Vision AutoencoderS (official repository for characterization of tumor heterogeneity through segmentation-free representation learning on multiplexed imaging data).