Software

• Keris - “kernel of integrated single cells”, a framework for identifying systematic variation at the single-cell level by leveraging low-resolution population-level data. By inferring cell-type-specific moments and their variation across conditions using large tissue-level bulk data representing a population, Keris allows us to generate testable hypotheses at the single-cell level that would otherwise require collecting single-cell data from a large number of donors. [GitHub] [paper]

• TCA - Tensor Composition Analysis (TCA) allows the deconvolution of two-dimensional data (observations by features) coming from a mixture of heterogeneous sources into a three-dimensional tensor of signals (observations by features by sources). In the context of genomics, TCA can deconvolve tissue-level bulk data (individuals by features) into a tensor of cell-type-specific levels for each individual (individuals by features by cell types) and it allows one to detect cell-type-specific statistical relations (associations) with an outcome of interest. [GitHub] [paper]

• BayesCCE - Bayesian Cell Count Estimation, a reference-free, semi-supervised method for estimating cell-type proportions from DNA methylation data collected from heterogeneous sources by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue. [GitHub] [paper]

• GLINT - A user-friendly command-line toolset for fast analysis of genome-wide DNA methylation data. GLINT, which does not require any programming proficiency, allows an easy execution of Epigenome-Wide Association Study (EWAS) analysis pipeline under different statistical models while accounting for known confounders in methylation data. [GitHub] [paper]

• EPISTRUCTURE - A reference-based algorithm for the inference of ancestry information from methylation data, without the need for genetic data. EPISTRUCTURE is based on an observation that ancestry is mirrored in genome-wide DNA methylation data and that it can be further isolated more effectively by leveraging the correlation structure of methylation CpGs with cis-located SNPs. EPISTRUCTURE is available via GLINT (See above). [paper]

• ReFACTor - Reference-Free Adjustment for Cell-Type composition, a sparse principal component analysis (PCA) under a column-sparse model. In the context of DNA methylation analysis, ReFACTor allows one to capture and correct for cell-type heterogeneity in an unsupervised manner. [GitHub] [paper]