single-cell RNA-seq
Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method
... a cell-to-cell distance matrix from individ- ual K-means clustering to get a consensus ...two single cell RNA-seq datasets [GSE72056 and GSE73727], as they contained preexisting ...
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Single-cell RNA-seq data analysis using Chipster
... What are the main analysis steps for clustering cells and finding cluster marker genes 6... Single cell RNA-seq.[r] ...
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Simulation based benchmarking of isoform quantification in single cell RNA seq
... The second simulation method was based on two tools, Splatter and Polyester. A flowchart showing the steps followed to generate the Splatter- and Polyester-simulated data is displayed in Fig. 1. Splatter is a simulation ...
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Feature selection and dimension reduction for single cell RNA Seq based on a multinomial model
... Single-cell RNA-Seq (scRNA-Seq) is a powerful tool for profiling gene expression patterns in individual cells, facil- itating a variety of analyses such as identification of novel ...
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Clustering of small - sample single - cell RNA - seq data via feature clustering and selection
... We have presented FeatClust, a software tool for clustering and visualisation of small sample size single-cell RNA-seq datasets containing high dimensionality. The method is based on feature ...
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Fast and accurate single cell RNA seq analysis by clustering of transcript compatibility counts
... a single-cell RNA-seq experiment, fur- ther biological interpretation of the results (marker gene identification or differential expression) requires some form of quantification of expression ...
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Single cell RNA seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
... construction Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell ...the single cells, a mouth ...
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CEL Seq2: sensitive highly multiplexed single cell RNA Seq
... Single-cell transcriptomics is a transformative method with tremendous potential to illuminate the complexities of gene regulation. Single-cell RNA-Seq was first intro- duced by ...
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BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
... from single-cell RNA-seq ...B cell that is present at low frequencies in blood under steady-state conditions, but these cells undergo a rapid, transient expansion approximately 4–7 days ...
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Single-Cell RNA-seq Identifies Cell Subsets in Human Placenta That Highly Expresses Factors to Drive Pathogenesis of SARS-CoV-2
... a single cell, the Y axis represents Transcripts Per Million ...a single ACE2+TMPRSS2+ cell of the second trimester extravillous ...from single cell RNA-seq of ...
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Psychrophilic proteases dramatically reduce single cell RNA seq artifacts: a molecular atlas of kidney development
... kidney single-cell RNA- seq data generates the cell groupings shown in ...following single-cell dissociation, it is possible to assign cell types to the resulting ...
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Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
... Single-cell RNA-Seq (scRNA-Seq) has proved to be a powerful tool for probing cell states [1–5], defining cell types [6–9], and describing cell lineages ...each ...
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Vireo: Bayesian demultiplexing of pooled single cell RNA seq data without genotype reference
... 3’ single- cell RNA-seq data from the 10x Genomics platform (v2 kit) for 16 genetically distinct samples from the census of immune cells project that are available from the Human Cell ...
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Single cell RNA seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
... To assess potential genomic DNA contamination, we sequenced oocyte samples both with and without the nu- clear region removed. There was no significant difference in the percentage of reads mapped to exons, introns and ...
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CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA seq data
... Applying CellSIUS to this data identified 7 subpopula- tions (Fig. 5c, d). Notably, within the mixed glial cells (G), CellSIUS identified a rare subgroup (1.1% of total population, G.sub_1) characterized by a signature ...
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SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... Single-cell RNA sequencing (scRNA-seq) has revolution- ized cell biology, enabling studies of heterogeneity and transcriptome dynamics of complex tissues at single-cell ...
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MetaCell: analysis of single cell RNA seq data using K nn graph partitions
... sampled cell types show additional hidden structure and potential remaining outlier ...multiple cell types, perhaps representing technical experimental ...a cell-type specific fashion, for example ...
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Single cell RNA seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
... codon was cloned into the targeting vector backbone (modified from Addgene 31938) [75]. FseI and SacI linearized T-2A-EGFP-PGK-Puro cassettes were used for gene targeting experiments. All the DNA oligos used in this ...
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SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA seq data
... from cell to cell in a systematic ...starting cell and uses the geodesic entropy values to detect the presence, number, and location of branches in the cellular trajectory ...
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DeepImpute: an accurate, fast, and scalable deep neural network method to impute single cell RNA seq data
... 5 cell types (proportions: ...separates cell types on the simulation, closely followed by scImpute ...each cell type and compared with the true differentially expressed ...
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