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Adaptive signal recovery on graphs via harmonic analysis for experimental design in neuroimaging

Magellan: toward building entity matching management systems

Magellan

Magellan is a set of tools and how-to guides for developing entity-matching systems. The Magellan tools are built on the Python data science and big data eco-system, and aim to cover the entire entity-matching pipeline.

Baseline regularization for computational drug repositioning with longitudinal observational data

EBSeqHMM

EBSeqHMM is an R package that implements an auto-regressive hidden Markov model for identifying genes and isoforms that have expression changes in ordered RNA-seq experiments, and clustering the identified genes into paths showing similar changes. EBSeqHMM is suitable for any ordered RNA-seq experiment including time courses and spatially ordered experiments.

Oscope

Oscope is a statistical pipeline for identifying oscillatory genes and characterizing one cycle of their oscillation, referred to as a base-cycle, in unsynchronized snapshot single cell RNA-seq experiments. The Oscope pipeline includes three modules: a paired-sine model module to identify candidate oscillator pairs; a clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to estimate the base-cycle oscillation within each group.

OEFinder

OEFinder is an R package that allows an investigator to identify genes having the so-called ordering effect in single-cell RNA-seq data generated by the Fluidigm C1 platform. This effect (Leng et al., Nature Methods, 2015) refers to significantly increased gene expression in cells captured from sites with small or large plate output IDs.

Rolemodel

The role model is a probability model used in the context of gene set analysis to describe the functional content of a user-supplied gene list, such as one derived from a genome-wide experiment. It integrates the list with gene sets from a knowledge base (e.g. Gene Ontology) and aims to summarize gene functions that are represented at an unusually high rate on the list. Compared to other gene-set enrichment analysis schemes, role model calculations contend better with the complexity of the knowledge base, including redundancies caused by overlapping sets and the effects of set-size variation.

Computational drug repositioning using continuous self-controlled case series

Latent variable graphical model selection using harmonic analysis: applications to the Human Connectome Project (HCP)

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