matlabs r2016a built-in mle function Search Results


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application econometrics toolbox  (MathWorks Inc)
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jmp software cary, version 9.0  (SAS institute)
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machine learning toolbox  (MathWorks Inc)
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Machine Learning Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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dataview software  (Becton Dickinson)
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Becton Dickinson dataview software
Single-cell RNA-seq analysis of sorted CD4 + T cells and ILCs from human peripheral blood. ( a ) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4 + T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. ( b ) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7 , CCL5 , PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. ( d ) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD <t>DataView</t> software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. ( f ) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. ( g ) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. ( h ) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.
Dataview Software, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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jmp software  (SAS institute)
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SAS institute jmp software
Single-cell RNA-seq analysis of sorted CD4 + T cells and ILCs from human peripheral blood. ( a ) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4 + T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. ( b ) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7 , CCL5 , PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. ( d ) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD <t>DataView</t> software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. ( f ) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. ( g ) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. ( h ) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.
Jmp Software, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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prism 8  (GraphPad Software Inc)
90
GraphPad Software Inc prism 8
Single-cell RNA-seq analysis of sorted CD4 + T cells and ILCs from human peripheral blood. ( a ) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4 + T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. ( b ) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7 , CCL5 , PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. ( d ) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD <t>DataView</t> software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. ( f ) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. ( g ) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. ( h ) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.
Prism 8, supplied by GraphPad Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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phansalkar thresholding algorithm  (Dolby Laboratories)
90
Dolby Laboratories phansalkar thresholding algorithm
Single-cell RNA-seq analysis of sorted CD4 + T cells and ILCs from human peripheral blood. ( a ) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4 + T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. ( b ) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7 , CCL5 , PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. ( d ) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD <t>DataView</t> software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. ( f ) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. ( g ) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. ( h ) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.
Phansalkar Thresholding Algorithm, supplied by Dolby Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Single-cell RNA-seq analysis of sorted CD4 + T cells and ILCs from human peripheral blood. ( a ) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4 + T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. ( b ) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7 , CCL5 , PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. ( d ) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD DataView software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. ( f ) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. ( g ) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. ( h ) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.

Journal: JID Innovations

Article Title: Dupilumab Effects on Innate Lymphoid Cell and Helper T Cell Populations in Patients with Atopic Dermatitis

doi: 10.1016/j.xjidi.2021.100003

Figure Lengend Snippet: Single-cell RNA-seq analysis of sorted CD4 + T cells and ILCs from human peripheral blood. ( a ) Th2 cells are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-seq data of 6,402 CD4 + T cells combined from six samples (before [Pre] and 16 weeks after [Post] dupilumab treatment from patient IDs 895, 918, and 939). Hierarchical clustering based on gene expression profiles was performed, and the T cells split into four clusters: naive T, Th1/17, Th2, and Treg. ( b ) Heatmaps of the representative genes from each cluster, naive T, Th1/17, Th2, and Treg. (c) Single-gene expression t-SNE plots of the single-cell RNA-Seq data. CCR7 , CCL5 , PTGDR2 (CRTH2), and FOXP3 are markers of naive T cells, Th1/17 cells, Th2 cells, and Treg cells, respectively. ( d ) Heatmaps of the representative genes (selected by differential expression analysis) gated on the Th2 cluster using the BD DataView software (n = 3, patient IDs 895, 918, and 939). (e) ILC2s are identified by single-cell RNA-seq. t-SNE plot of the single-cell RNA-Seq data of 638 ILCs combined from six samples (patient IDs 924 Pre/Post, 938 Pre/Post, 1049 Post, and 1062 Post). Hierarchical clustering based on gene expression profiles was performed, and the ILCs split into three clusters: NK/ILC1, ILC2, and ILC3. ( f ) Heatmaps of the representative genes from each cluster, NK/ILC1, ILC2, and ILC3. ( g ) Single-gene expression t-SNE plots of the single-cell RNA-seq data. PTGDR2 (CRTH2), KIT, and GZMK are markers of naive ILC2s, ILC3s, and NK/ILC1, respectively. ( h ) Heatmaps of the representative genes (selected by differential expression analysis) gated on ILC2 cluster using the BD DataView software (n = 2, patient IDs 924 and 938). ID, identification; ILC, innate lymphoid cell; max, maximum; min, minimum; RNA-seq, RNA sequencing; Th, T helper type; Treg, regulatory T cell; t-SNE, t-distributed stochastic neighbor embedding.

Article Snippet: All analyses were performed in BD DataView software using MATLAB (R2014a, MathWorks, Natick, MA) ( ) built-in cluster function with the maxclust option, according to the manufacturer’s instructions.

Techniques: RNA Sequencing Assay, Expressing, Software