scE2G_v1.3

Version of scE2G used for revisions of Sheth, Qiu, et al. 2024

Major changes from v1.2:

• Suggest users perform a shallow clone to reduce the file size of the clone in README.
• Added configuration options for parallel computing of Kendall correlation to increase computational speed.
• Fixed issues in the quality control report.

scE2G_v1.2

Version of scE2G used for revisions of Sheth, Qiu, et al. 2024

Major changes from v1.0:

• Map gene names from RNA matrix through Ensembl ID to provided gene and TSS reference files
• Retrain models for ATAC-only and multiome inputs with power law contact estimation (scATAC_powerlaw_v3 and multiome_powerlaw_v3)
• Add configuration options to provide RNA matrix with all cells (rather than exact set of cells for the cluster) and preprocessed fragment files
• Improve reporting of prediction properties, gene expression metrics, and other quality control measures
• Improve documentation of input file formats and pipeline outputs

scE2G_v1.0

Version of scE2G used for preprint Sheth, Qiu, et al. 2024 (add link)