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How to plot two heatmaps with the same cell height and width for two different Matrix (same column number but different row number) using heatmap.2 ?
heatmap heatmap.2
2.9 years ago by FantasticAI ▴ 60
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Weird output of DESeq2 when using single one sample from one group agains the other group (6 samples), really need some help
WaldTest DESeq2 NegativeBinomial
updated 2.9 years ago by 86k • written 2.9 years ago by ▴ 60
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Comment: Comment: DESeq2 modelling and Wald's test
2.9 years ago by FantasticAI ▴ 60
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Map mouse RNA-seq Ensembl gene ids to "org.Mm.eg.db", but get some "UNKNOWN" gene symbol, like "NA..25729", is it normal?
DEseq2 rna-seq DEG
updated 3.1 years ago by 3.2k • written 3.1 years ago by ▴ 60
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Comment: Comment: Weird output of geneCount for STAR?
3.1 years ago by FantasticAI ▴ 60
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STAR for mouse RNA-seq alignment, which parameters should I use besides the basic ones in practice?
reference STAR rna-seq genome
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: Weird output of geneCount for STAR?
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: STAR two -pass mode - lower alignment rate than one pass mode?
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: Weird output of geneCount for STAR?
3.1 years ago by FantasticAI ▴ 60
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Weird output of geneCount for STAR?
reference STAR rna-seq genome
updated 3.1 years ago by 13k • written 3.1 years ago by ▴ 60
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Comment: Comment: RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, wh
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, wh
3.1 years ago by FantasticAI ▴ 60
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RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, which reference genome should I download when using STAR aligner?
reference STAR rna-seq genome
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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7.2k
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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7.2k
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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7.2k
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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Comment: Comment: MultiQC report on sequence duplication levels for RNA-seq data, I think there mi
3.1 years ago by FantasticAI ▴ 60
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7.2k
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MultiQC report on sequence duplication levels for RNA-seq data, I think there might be some poor quality issues for my data, if so, how to fix it?
rna-seq
updated 3.1 years ago by 102k • written 3.1 years ago by ▴ 60
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Comment: Comment: How to interpret this duplicate sequence plot from FastQC
3.1 years ago by FantasticAI ▴ 60
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How to control the order of cells in dittoHeatmap for scRNAseq data analysis?
Cell scRNA dittoHeatmap Single
3.4 years ago by FantasticAI ▴ 60
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Comment: Comment: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
3.6 years ago by FantasticAI ▴ 60
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Using Seurat function `FindMarkers` to find differentially expressed genes between normal group and treatment group within one specific cell type clu…
Seurat FindMarkers scRNA
updated 3.6 years ago by 86k • written 3.6 years ago by ▴ 60
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Comment: Comment: I tried to convert SingleCellExperiment to Seurat Object, but it does not work,
3.6 years ago by FantasticAI ▴ 60
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I tried to convert SingleCellExperiment to Seurat Object, but it does not work, and keep return error: Error in .subset2(x, i, exact = exact) : subsc…
scRNA Seurat
updated 3.6 years ago by 86k • written 3.6 years ago by ▴ 60
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Comment: Comment: What is current the best available rat lung single cell RNA seq dataset for cel
3.6 years ago by FantasticAI ▴ 60
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Comment: Comment: What does it mean of de.genes in SingleR output? What is the difference between
3.6 years ago by FantasticAI ▴ 60
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Comment: Comment: What does it mean of de.genes in SingleR output? What is the difference between
3.6 years ago by FantasticAI ▴ 60
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What is current the best available rat lung single cell RNA seq dataset for cell type annotation? any recommendations ?
SingleR scRNAseq
3.6 years ago by FantasticAI ▴ 60
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I use SingleR to get cell type annotation for each cell, then try to annotate each cluster, but the clustering result seems not to be consistent with…
SingleR scRNAseq
3.6 years ago by FantasticAI ▴ 60
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2.3k
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Comment: Comment: What does it mean of de.genes in SingleR output? What is the difference between
3.6 years ago by FantasticAI ▴ 60
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What does it mean of de.genes in SingleR output? What is the difference between the genes in de.genes and genes in findMarkers?
SingleR scRNAseq
3.6 years ago by FantasticAI ▴ 60
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Comment: Comment: SingleR for integrated scRNA-seq analysis
3.6 years ago by FantasticAI ▴ 60
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4.4k
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Comment: Comment: SingleR for integrated scRNA-seq analysis
3.6 years ago by FantasticAI ▴ 60
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Comment: Comment: How to plot the heat map of a subset of cell types using plotHeatmap from scater
3.6 years ago by FantasticAI ▴ 60
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How to plot the heat map of a subset of cell types using plotHeatmap from scater package
scRNAseq scRNA SingleR plotHeatmap scater
3.6 years ago by FantasticAI ▴ 60
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Comment: Comment: How to plot the heat map of a subset of cell types using plotHeatmap from scater
3.6 years ago by FantasticAI ▴ 60
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1.4k
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Answer: Answer: is it normal to have zero mitochondria genes counts in my 10X data which is from
3.6 years ago by FantasticAI ▴ 60
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is it normal to have zero mitochondria genes counts in my 10X data which is from Cellranger 5.0 count?
10X scRNAseq
updated 3.6 years ago by 13k • written 3.6 years ago by ▴ 60
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Comment: Comment: How to ID cell types using reference scRNAseq dataset
3.6 years ago by FantasticAI ▴ 60
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1.2k
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Comment: Comment: How to ID cell types using reference scRNAseq dataset
3.6 years ago by FantasticAI ▴ 60
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5.9k
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Comment: Comment: the analysis of multiple samples of 10X scRNA-seq
3.6 years ago by FantasticAI ▴ 60
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How to ID cell types using reference scRNAseq dataset
Seurat groups scRNAseq
3.6 years ago by FantasticAI ▴ 60
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0
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4.4k
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Comment: Comment: Fraction reads in cells CELLRANGER
3.6 years ago by FantasticAI ▴ 60
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