scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation

Model-Based Approach to the Joint Analysis of Single-Cell Data on Chromatin Accessibility and Gene Expression

(2020) Zhixiang Lin et al.   STATISTICAL SCIENCE

Integrative Methods and Practical Challenges for Single-Cell Multi-omics

(2020) Anjun Ma et al.   TRENDS IN BIOTECHNOLOGY

Coupled co-clustering-based unsupervised transfer learning for the integrative analysis of single-cell genomic data

(2020) Pengcheng Zeng et al.   BRIEFINGS IN BIOINFORMATICS

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

(2019) Carmen Bravo González-Blas et al.   NATURE METHODS

Finite mixture-of-gamma distributions: estimation, inference, and model-based clustering

(2019) Derek S. Young et al.   Advances in Data Analysis and Classification

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Virtual methylome dissection facilitated by single-cell analyses

(2019) Liduo Yin et al.   Epigenetics & Chromatin

SCALE method for single-cell ATAC-seq analysis via latent feature extraction

(2019) Lei Xiong et al.   Nature Communications

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

(2018) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unsupervised clustering and epigenetic classification of single cells

(2018) Mahdi Zamanighomi et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations

(2018) Tony Hui et al.   Stem Cell Reports

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Semisoft clustering of single-cell data

(2018) Lingxue Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

Higher order methylation features for clustering and prediction in epigenomic studies

(2016) Chantriolnt-Andreas Kapourani et al.   BIOINFORMATICS

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Beta Regression inR

(2015) Francisco Cribari-Neto et al.   Journal of Statistical Software

Extended Beta Regression inR: Shaken, Stirred, Mixed, and Partitioned

(2015) Bettina Grün et al.   Journal of Statistical Software