Learning single-cell chromatin accessibility profiles using meta-analytic marker genes
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac541
Abstract: Motivation Single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) is a valuable resource to learn cis-regulatory elements such as cell-type specific enhancers and transcription factor binding sites. However, cell-type identification of scATAC-seq data is… read more here.
Keywords: scatac seq; marker genes; cell; seq ... See more keywords
scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac739
Abstract: Abstract Motivation Technological advances have enabled us to profile single-cell multi-omics data from the same cells, providing us with an unprecedented opportunity to understand the cellular phenotype and links to its genotype. The available protocols… read more here.
Keywords: seq data; cell; scrna seq; seq ... See more keywords
Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets
Sign Up to like & getrecommendations! Published in 2020 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa349
Abstract: Abstract While the methods available for single-cell ATAC-seq analysis are well optimized for clustering cell types, the question of how to integrate multiple scATAC-seq data sets and/or sequencing modalities is still open. We present an… read more here.
Keywords: data sets; seq data; biology; scatac seq ... See more keywords
scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology"
DOI: 10.1101/2021.04.16.440230
Abstract: It is a challenging task to integrate scRNA-seq and scATAC-seq data obtained from different batches. Existing methods tend to use a pre-defined gene activity matrix to convert the scATAC-seq data into scRNA-seq data. The pre-defined… read more here.
Keywords: seq data; scrna seq; seq; seq scatac ... See more keywords
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation
Sign Up to like & getrecommendations! Published in 2022 at "PLOS Computational Biology"
DOI: 10.1101/2022.11.23.517534
Abstract: Single cell ATAC-seq (scATAC-seq) enables the mapping of regulatory elements in fine-grained cell types. Despite this advance, analysis of the resulting data is challenging, and large scale scATAC-seq data are difficult to obtain and expensive… read more here.
Keywords: seq data; scatac seq; single cell; cell ... See more keywords
GAGAM v1.2: An Improvement on Peak Labeling and Genomic Annotated Gene Activity Matrix Construction
Sign Up to like & getrecommendations! Published in 2022 at "Genes"
DOI: 10.3390/genes14010115
Abstract: Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is rapidly becoming a powerful technology for assessing the epigenetic landscape of thousands of cells. However, the sparsity of the resulting data poses significant challenges to their… read more here.
Keywords: activity matrix; gagam; gene activity; scatac seq ... See more keywords