LAUSR

About LAUSR
Donate
Contact Us

Follow us:

You are not signed in:

Sign Up!


   Articles with "scatac seq" as a keyword



Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS

Sign Up to like & get
recommendations! Published in 2025 at "Nature Communications"

DOI: 10.1038/s41467-024-55580-5

Abstract: Single cell ATAC-seq (scATAC-seq) experimental designs have become increasingly complex, with multiple factors that might affect chromatin accessibility, including genotype, cell type, tissue of origin, sample location, batch, etc., whose compound effects are difficult to… read more here.

Keywords: seq data; chromatin accessibility; pacs; scatac seq ... See more keywords

Learning single-cell chromatin accessibility profiles using meta-analytic marker genes

Sign Up to like & get
recommendations! 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 & get
recommendations! 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 & get
recommendations! 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 & get
recommendations! 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 & get
recommendations! 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 & get
recommendations! 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

Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects

Sign Up to like & get
recommendations! Published in 2024 at "International Journal of Molecular Sciences"

DOI: 10.3390/ijms25031479

Abstract: The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell… read more here.

Keywords: cell; plant science; scatac seq; plant ... See more keywords