🎯 New in Bioinformatics Advances: "TransPilot: Mining key transcription factors by correlating binding sites with differentially expressed genes"
See it here: https://doi.org/10.1093/bioadv/vbag145
GDIv2 updates the Gene Damage Index by correcting for coding sequence length and applying gene-specific CADD score normalization. Four implementations across 1kGP and gnomAD datasets substantially improved discrimination between disease-relevant and accessory genes over the original GDI.
TransPilot identifies key transcription factors from transcriptome data using ANN-scored, direction-annotated TF-target sets correlated against ranked DEG lists via weighted Kendall's tau.
🧬 New in Bioinformatics Advances: "Pylluminator: Fast and scalable analysis of DNA methylation data in Python"
Read it here: https://doi.org/10.1093/bioadv/vbag146
This study introduces Pylluminator, a Python toolkit for Illumina methylation array analysis covering pre-processing, QC, differential methylation, and visualization. Built on SeSAMe and ChAMP, it supports all major array versions and outperforms existing R packages in speed.
Bioinformatics Advances
🖥️ The TransPilot server is available at http://www.thua45.cn/transpilot.
Benchmarked on macrophage polarization data, it outperformed SCENIC, VIPER, and ChEA3 across the majority of tested transcription factors.
🗂️ GDIv2 resources are freely available at
🐍 Pylluminator is available at https://github.com/eliopato/pylluminator. Documentation at
