Software

QFM

R package · github.com/Kalhor-Lab/QFM · documentation and tutorials · Zenodo archive

Quantitative fate mapping from lineage barcodes. Phylotime reconstructs time-scaled cell phylogenies by maximum likelihood under a general model of barcode mutagenesis, and ICE-FASE infers the progenitor state hierarchy, commitment times, population sizes and commitment biases from them. Includes a simulator for cell phylogenies and lineage barcodes. Described in Fang et al., Cell 2022.

FUNCODE

Web application · jhubiostatistics.shinyapps.io/FUNCODE · code at github.com/wefang/funcode · scores on the ENCODE portal · preprint

Genome-wide scores of functional conservation between human and mouse regulatory elements, computed from 2,595 uniformly processed ENCODE datasets (DNase-seq, ATAC-seq and histone ChIP-seq) through in silico sample matching. The web application looks up any human or mouse region, by coordinates or a BED file, and returns its conserved partner elements and their scores. The repository holds the full pipeline, from mapping regions and integrating samples to computing the scores.

Browse the scores in the UCSC Genome Browser: human (hg38) · mouse (mm10)