[PDF] Top 20 SCANPY: large scale single cell gene expression data analysis
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SCANPY: large scale single cell gene expression data analysis
... show cell-type annotations obtained by comparisons with bulk ...marker gene for B cells in cluster 7, which agrees with the bulk ...root cell in the CD34+ cluster and detect a branching trajectory, ... See full document
5
Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data
... the analysis of single cell gene expression ...for single cell ...a large look-up ...experimental data by the lookup table, and then the maximum likelihood ... See full document
29
Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart
... Our data suggest that natural aging is also asso- ciated with such a change in fibroblast fates, leading to an increasing, but low, number of osteocalcin gene–expressing cells in the ...published ... See full document
18
Characterizing heterogeneity in leukemic cells using single cell gene expression analysis
... t-SNE analysis and unsupervised hierarchical clus- tering suggest that the transcriptomic state of leukemic cells is close to GMPs and far away from HSCs, support- ing a model in which LSCs are not directly linked ... See full document
13
Developmental fate and lineage commitment of singled mouse blastomeres
... these data, we employed principal component analysis (PCA) based on the expression of these genes in the TE, ICM and 1/32LS ...blastomere expression patterns onto component 1 and 2 clearly ... See full document
10
ZIFA: Dimensionality reduction for zero inflated single cell gene expression analysis
... larger data sets involving thousands of genes and hundreds of ...latent expression val- ues for zero measurements. If a gene has a very low frequency of expression and is zero across most ... See full document
10
scBFA: modeling detection patterns to mitigate technical noise in large scale single cell genomics data
... established cell type markers on the PBMC, HSCs, and Pancreatic benchmarks, for which clear markers could be ...S3-S5). Gene selection reduced the marker sets further to 30, 24, and 43 markers for HVG and ... See full document
20
The temporal and spatial analysis of single cell gene expression
... Under the LNA, the MCMC algorithm for this simulation took 400,000 iterations compared to the BDA methodology, which took 1,500,000 iterations to sufficiently explore the respective posteriors. The corresponding thinned ... See full document
257
SCALE: modeling allele specific gene expression by single cell RNA sequencing
... a cell, amplification and sequencing bias can be captured and estimated through the spike-in ...for Analysis of Single Cell data, unpublished), which explicitly models the technical ... See full document
15
Single-Cell Gene-Expression Analysis by Quantitative RT-PCR
... the cell types we surveyed and cardiomyocytes is the post-mitotic lifetime of the ...T cell populations in the peripheral blood are continuously renewed from the stem-cell pool in the bone ...stem ... See full document
225
Gene based Higher Criticism methods for large scale exonic single nucleotide polymorphism data
... with single- locus association analysis in genome-wide association studies, gene-based multiple-loci analysis explores the joint effect of genetic factors related to these func- tional units ... See full document
6
Large scale analysis of positional effects of single-base mismatches on microarray gene expression data
... Our results may be useful for improving future versions of microarray platform design, especially those which involve the single-base mismatches such as the Affymetrix Gen- eChip. On the one hand, these results ... See full document
13
GiniClust: detecting rare cell types from single cell gene expression data with Gini index
... The gene expression profiles were synthesized by using a strategy similar to that in the RaceID paper ...Specifically, gene expression levels within each cell cluster were modeled as ... See full document
13
Single-Cell Gene Expression Variation as A Cell-Type Specific Trait: A Study of Mammalian Gene Expression Using Single-Cell RNA Sequencing
... components analysis projection of the 91 cells largely segregates the five cell types (Figure ...examined expression levels for a curated list of marker mRNAs expected in serotonergic neurons, ... See full document
136
Inferring causal relations from multivariate time series : a fast method for large scale gene expression data
... In contrast, our study focuses on the small sample problem in gene expression data analysis. This paper aims at illustrating the application of multivariate time series analysis in the ... See full document
10
Single mammalian cell gene expression analysis using microfluidics
... discussing gene expression noise measurements, to this date, have measured the corresponding protein levels to study noise in the genes ...microarray data across ...assume cell distributions ... See full document
179
Statistical inference from large scale genomic data
... of gene regulatory networks, the ultimate goal of this type of ...for gene expression data is proposed to obtain tighter and potentially more informative gene ...of Gene Ontology ... See full document
206
Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions
... of single amino acid scanning ...scanning data we analyzed arises from genetic selections for protein ...the large-scale mutagenesis data sets we used were benchmarked against and found ... See full document
9
Novel prognostic genes of diffuse large B-cell lymphoma revealed by survival analysis of gene expression data
... for analysis with small sample size. The analysis procedure is as follows: 1) Put the samples in ascending order according to the survival time, rank i = 1, 2, …, ... See full document
7
A large-scale analysis study on the clinical and viral characteristics of hepatitis B infection with concurrence of hepatitis B surface or E antigens and their corresponding antibodies.
... Further large-scale, multi-center studies are needed to clarify the clinical implications of these serological patterns (HBsAg and anti-HBs positivity, or HBsAg and anti-HBs positivity), including specific ... See full document
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