Principal component analysis
Principal component analysis is a versatile statistical method for reducing a cases-by-
variables data table to its essential features, called principal components. Principal …
variables data table to its essential features, called principal components. Principal …
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
M Su, T Pan, QZ Chen, WW Zhou, Y Gong, G Xu… - Military Medical …, 2022 - Springer
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has
advanced our understanding of the pathogenesis of disease and provided valuable insights …
advanced our understanding of the pathogenesis of disease and provided valuable insights …
Biologically informed deep learning to query gene programs in single-cell atlases
M Lotfollahi, S Rybakov, K Hrovatin… - Nature Cell …, 2023 - nature.com
The increasing availability of large-scale single-cell atlases has enabled the detailed
description of cell states. In parallel, advances in deep learning allow rapid analysis of newly …
description of cell states. In parallel, advances in deep learning allow rapid analysis of newly …
ATTED-II v11: a plant gene coexpression database using a sample balancing technique by subagging of principal components
T Obayashi, H Hibara, Y Kagaya, Y Aoki… - Plant and Cell …, 2022 - academic.oup.com
Abstract ATTED-II (https://atted. jp) is a gene coexpression database for nine plant species
based on publicly available RNAseq and microarray data. One of the challenges in …
based on publicly available RNAseq and microarray data. One of the challenges in …
Analysis and visualization of spatial transcriptomic data
Human and animal tissues consist of heterogeneous cell types that organize and interact in
highly structured manners. Bulk and single-cell sequencing technologies remove cells from …
highly structured manners. Bulk and single-cell sequencing technologies remove cells from …
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Abstract We present pipeComp (https://github. com/plger/pipeComp), a flexible R framework
for pipeline comparison handling interactions between analysis steps and relying on multi …
for pipeline comparison handling interactions between analysis steps and relying on multi …
Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases
R Cuevas-Diaz Duran, JC González-Orozco… - Frontiers in Cell and …, 2022 - frontiersin.org
Neurodegenerative diseases affect millions of people worldwide and there are currently no
cures. Two types of common neurodegenerative diseases are Alzheimer's (AD) and …
cures. Two types of common neurodegenerative diseases are Alzheimer's (AD) and …
Deciphering the biology of circulating tumor cells through single-cell RNA sequencing: implications for precision medicine in cancer
S Orrapin, P Thongkumkoon, S Udomruk… - International Journal of …, 2023 - mdpi.com
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve
them in hematogenous dissemination. Studying CTCs systematically is technically …
them in hematogenous dissemination. Studying CTCs systematically is technically …
Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology
The rapid growth of large-scale spatial gene expression data demands efficient and reliable
computational tools to extract major trends of gene expression in their native spatial context …
computational tools to extract major trends of gene expression in their native spatial context …
Fast and accurate out-of-core PCA framework for large scale biobank data
Principal component analysis (PCA) is widely used in statistics, machine learning, and
genomics for dimensionality reduction and uncovering low-dimensional latent structure. To …
genomics for dimensionality reduction and uncovering low-dimensional latent structure. To …