Results 41 to 50 of about 86,859 (350)

constclust: Consistent Clusters for scRNA-seq [PDF]

, 2020
1AbstractUnsupervised clustering to identify distinct cell types is a crucial step in the analysis of scRNA-seq data. Current clustering methods are dependent on a number of parameters whose effect on the resulting solution’s accuracy and reproducibility are poorly understood. The adjustment of clustering parameters is therefore ad-hoc, with most users
Isaac Virshup, Jarny Choi, Kim-Anh Lê Cao, Christine A Wells   +3 more
openaire   +1 more source

Tumor Functional Heterogeneity Unraveled by scRNA-seq Technologies [PDF]

Trends in Cancer, 2020
Effective cancer treatment has been precluded by the presence of various forms of intratumoral complexity that drive treatment resistance and metastasis. Recent single-cell sequencing technologies are significantly facilitating the characterization of tumor internal architecture during disease progression.
González Silva, Laura, Quevedo Palacio, Laura, Varela Egocheaga, Ignacio   +2 more
openaire   +5 more sources

ScRNA-seq and ST-seq in liver research

Cell Regeneration, 2023
AbstractSpatial transcriptomics, which combine gene expression data with spatial information, has quickly expanded in recent years. With application of this method in liver research, our knowledge about liver development, regeneration, and diseases have been greatly improved.
Jia He, Chengxiang Deng, Leonard Krall, Zhao Shan   +3 more
openaire   +3 more sources

Compression of quantification uncertainty for scRNA-seq counts [PDF]

Bioinformatics, 2020
Abstract Motivation Quantification estimates of gene expression from single-cell RNA-seq (scRNA-seq) data have inherent uncertainty due to reads that map to multiple genes. Many existing scRNA-seq quantification pipelines ignore multi-mapping reads and therefore underestimate expected read ...
Scott Van Buren, Hirak Sarkar, Avi Srivastava, Naim U. Rashid, Rob Patro, Michael I. Love   +5 more
openaire   +2 more sources

Comparative Analysis of Single-cell and Single-nucleus RNA-sequencing in a Rabbit Model of Retinal Detachment-related Proliferative Vitreoretinopathy

Ophthalmology Science, 2023
Purpose: Proliferative vitreoretinopathy (PVR) is the most common cause of failure of retinal reattachment surgery, and the molecular changes leading to this aberrant wound healing process are currently unknown.
Clayton P. Santiago, PhD, MS, Megan Y. Gimmen, BSc, Yuchen Lu, BSc, Minda M. McNally, MS, Leighton H. Duncan, MA, BSc, Tyler J. Creamer, PhD, Linda D. Orzolek, MS, Seth Blackshaw, PhD, Mandeep S. Singh, MD, PhD   +8 more
doaj   +1 more source

Comparison of scRNA-seq data analysis method combinations

Briefings in Functional Genomics, 2022
AbstractSingle-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data analysis refers to the use of appropriate methods to analyze the dataset generated by RNA-sequencing performed on the single-cell transcriptome. It usually contains three steps: normalization to eliminate the technical noise, dimensionality reduction to facilitate visual ...
Li Xu, Tong Xue, Weiyue Ding, Linshan Shen   +3 more
openaire   +2 more sources

Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE

Genome Biology, 2023
Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched short-read data to identify cell barcodes. We
Yupei You, Yair D. J. Prawer, Ricardo De Paoli-Iseppi, Cameron P. J. Hunt, Clare L. Parish, Heejung Shim, Michael B. Clark   +6 more
doaj   +1 more source

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin. [PDF]

, 2017
Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcriptomic analyses have previously been performed from bulk skin samples or from epithelial and immune cells expanded in cell culture.
Ahn, Richard S, Arron, Sarah T, Chang, David S, Gupta, Rashmi, Lai, Kevin, Lee, Kristina M, Liao, Wilson, Nititham, Joanne, Rosenblum, Michael, Taravati, Keyon   +9 more
core   +1 more source

Applications of single‐cell sequencing for the field of otolaryngology: A contemporary review

Laryngoscope Investigative Otolaryngology, 2020
Objectives Single‐cell RNA sequencing (scRNA‐Seq) is a new technique used to interrogate the transcriptome of individual cells within native tissues that have already resulted in key discoveries in auditory basic science research. Rapid advances in scRNA‐
Madeline P. Pyle, Michael Hoa
doaj   +1 more source

Generalized gene co-expression analysis via subspace clustering using low-rank representation [PDF]

, 2019
BACKGROUND: Gene Co-expression Network Analysis (GCNA) helps identify gene modules with potential biological functions and has become a popular method in bioinformatics and biomedical research.
Huang, Kun, Wang, Tongxin, Zhang, Jie
core   +1 more source