chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

Schep, Alicia N, Wu, Beijing, Buenrostro, Jason D, Greenleaf, William J·2017·Nature Methods

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  12. Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data
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  15. scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data
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  16. Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development
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  18. Developmental dynamics of the neural crest–mesenchymal axis in creating the thymic microenvironment
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  21. Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation
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  26. Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator
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  29. Integration site–dependent HIV-1 promoter activity shapes host chromatin conformation
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  31. Joint trajectory inference for single-cell genomics using deep learning with a mixture prior
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  32. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions
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  38. Destin: toolkit for single-cell analysis of chromatin accessibility
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  46. Computational tools for inferring transcription factor activity
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  56. Unbiased integration of single cell multi-omics data
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  68. Functional genomic approaches to elucidate the role of enhancers during development
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  69. Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue
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  72. Analytical Approaches for ATAC‐seq Data Analysis
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  77. Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging
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  85. Coupled co-clustering-based unsupervised transfer learning for the integrative analysis of single-cell genomic data
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