[PDF] Top 20 Classification of low quality cells from single cell RNA seq data
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Classification of low quality cells from single cell RNA seq data
... broken cells can be wrongly annotated and even seemingly empty capture sites may contain enough RNA to yield high gene ...mES cells. As we are performing this analysis on only one cell type, ... See full document
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scPred: accurate supervised method for cell type classification from single cell RNA seq data
... test data, we obtained a sensitivity of ...that cell-type ...non-tumor cells to ob- tain a set of discriminant ...same data partitions used ...of cells of a given cell type on ... See full document
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A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
... of cells is dependent on the number of distinct cell states within the population, the required sequencing depth also depends on the mag- nitude of differences between these ...unbiased cell-type ... See full document
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CEL Seq2: sensitive highly multiplexed single cell RNA Seq
... fibroblast cells carrying a CyclinB1-GFP fusion reporter [12] and compared this to data obtained using the original protocol (with the single modification that the primers contained ...24 ... See full document
7
Normalization and variance stabilization of single cell RNA seq data using regularized negative binomial regression
... normalize single-cell ...residuals from this model as normalized expression ...given cell indicate that we observed more UMIs than expected given the gene’s average expres- sion in the ... See full document
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Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
... major RNA sequencing ...platforms. RNA-Seq of polyadenylated RNAs (A) or total RNA after rRNA depletion (B) enables profiling at a high resolution but requires a well-curated reference genome ... See full document
9
CIDR: Ultrafast and accurate clustering through imputation for single cell RNA seq data
... scRNA-seq data and does not address the issue of ...of single cells into meaningful groups or ...large data sets of more than several hundred single ... See full document
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Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis
... at single cell ...epithelial cell isolation, sorting and single cell RNA ...of cells positive for Ngn3 (Neurog3 expression >0) and negative for Ngn3 (no Neurog3 ... See full document
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Genotype free demultiplexing of pooled single cell RNA seq
... files from three individual samples ...prediction from scSplit compared to demuxlet (TPR/FDR: ...per cell in order to test the performance under low sequencing depth and the over- all result ... See full document
12
Simulation based benchmarking of isoform quantification in single cell RNA seq
... eXpress’s low precision is due to it being too liberal when calling isoforms as ...per cell was twice as high for eXpress, which called an aver- age of 41,372 isoforms as expressed per cell, as for ... See full document
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MetaCell: analysis of single cell RNA seq data using K nn graph partitions
... T cells, NK cells, B cells, myeloid cells, megakaryocytes, and progenitor ...T cells, the variable MHC-I expression (HLA-A,HLA-C) in different cell sub-types (group [6]), ... See full document
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Single cell mRNA sequencing identifies subclonal heterogeneity in anti cancer drug responses of lung adenocarcinoma cells
... interpreting single cell RNA-seq data, the data quality needs to be considered, because of the high mag- nitude of amplification in the sequencing ...calls. RNA ... See full document
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Vireo: Bayesian demultiplexing of pooled single cell RNA seq data without genotype reference
... on data from multiplexed human ...genotype data and Demuxlet applied with complete genotype ...of cells assigned to each sample, either considering cells that were consistently assigned ... See full document
12
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS seq) assay
... ATAC- seq is inherent in the method design, and is mainly due to three ...typical cells, and the regions in which two adjacent transposition events are too far apart cannot be amplified by ...captures ... See full document
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CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA seq data
... neural cell types of early human cortico- genesis such as cycling and quiescent NPs, EOMES + IPs, CR cells, immature and mature neurons with a transcrip- tional identity indicative of layer V/VI neurons, ... See full document
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SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... simulated data using bulk RNA-seq data We used the bulk RNA-seq dataset of mouse hair folli- cles from ...genes from 20,721 genes in the above data matrices. ... See full document
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SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA seq data
... a cell to the same position in a ...cascade, cells could reach a final end state through sev- eral distinct sequences of gene expression ...if cells within a single initial population receive ... See full document
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PHLI seq: constructing and visualizing cancer genomic maps in 3D by phenotype based high throughput laser aided isolation and sequencing
... tumor cells that acquired advantageous fitness after undergoing an oncogenic initial mutation ...of cells from different subclones in a tumor mass separately, these approaches relied upon computa- ... See full document
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Single cell epigenomic variability reveals functional cancer heterogeneity
... of cells defined by single-cell chromatin activity. Data mining of available knockdown as well as scRNA-seq data allow correlation of cell surface marker expression with ... See full document
12
Revealing cellular and molecular transitions in neonatal germ cell differentiation using single cell RNA sequencing
... stem cell-progenitor-differentiation-primed spermatogonia transition is reminiscent of the adult differentiation trajectory reported recently (Green et ...I cells (including stem cells) expressed a ... See full document
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