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Comment: C: Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
3.7 years ago lirongrossmann ▴ 80
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6
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2.6k
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 80
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Comment: C: Cluster location in UMAP using SingleCellExperiment and SingleR
3.7 years ago lirongrossmann ▴ 80
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1.3k
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Comment: C: Raw counts for reference dataset in single cell rnaseq
3.7 years ago lirongrossmann ▴ 80
1
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3
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1.3k
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Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 80
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1.3k
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Comment: C: marker genes in single cell experiment
3.7 years ago lirongrossmann ▴ 80
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1.5k
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Comment: C: most correlated genes in SingleR
3.7 years ago lirongrossmann ▴ 80
0
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0
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753
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Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.7 years ago lirongrossmann ▴ 80
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0
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2.1k
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Comment: C: Trajectory analysis for single cell sequencing
3.8 years ago lirongrossmann ▴ 80
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1
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2.1k
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Comment: C: Trajectory analysis for single cell sequencing
3.8 years ago lirongrossmann ▴ 80
0
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1
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1.3k
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Handling outliers in Deseq2
outliers deseq2 logfoldchange
6.3 years ago lirongrossmann ▴ 80
9
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2
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5.4k
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log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold deseq2
updated 6.4 years ago by 42k • written 6.4 years ago by ▴ 80
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1
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1.3k
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Base mean count threshold
deseq2 base
updated 6.4 years ago by 42k • written 6.4 years ago by ▴ 80
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1
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3.2k
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Comment: C: Batch effect removal with Deseq2
6.4 years ago lirongrossmann ▴ 80
1
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3
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3.2k
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Batch effect removal with Deseq2
deseq2 batch effect removebatcheffect() limma
updated 6.4 years ago by 42k • written 6.4 years ago by ▴ 80
2
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2
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4.2k
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choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 6 months ago by • 0 • written 6.4 years ago by ▴ 80
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0
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1.5k
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Answer: A: an unexplained phenomenon using variance stabilizing transformation for downstre
6.4 years ago lirongrossmann ▴ 80
1
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2
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1.5k
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an unexplained phenomenon using variance stabilizing transformation for downstream analysis
variancestabilizingtransformation normalization
6.4 years ago lirongrossmann ▴ 80
1
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1
reply
724
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NA adjp with extremely low p value
deseq2 adjusted pvalue
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 80
0
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1
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1.3k
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Distribution of transformed data using VST
variancestabilizingtransformation deseq2
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 80
0
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1
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483
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Deseq2 for small matched samples
deseq2
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 80
0
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1
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1.6k
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Comment: C: calculating logfold change from variance stabilizing transformation
6.6 years ago lirongrossmann ▴ 80
0
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1
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1.6k
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Comment: C: calculating logfold change from variance stabilizing transformation
6.6 years ago lirongrossmann ▴ 80
2
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5
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1.6k
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calculating logfold change from variance stabilizing transformation
deseq2 logfoldchange variancestabilizingtransformation
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 80
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0
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2.5k
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Comment: C: comparing strand-specific counts to unstranded counts
6.6 years ago lirongrossmann ▴ 80
0
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1
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2.5k
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Comment: C: comparing strand-specific counts to unstranded counts
6.6 years ago lirongrossmann ▴ 80
0
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1
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2.5k
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Comment: C: comparing strand-specific counts to unstranded counts
6.6 years ago lirongrossmann ▴ 80
0
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1
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2.5k
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Comment: A: comparing strand-specific counts to unstranded counts
6.6 years ago lirongrossmann ▴ 80
2
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8
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2.5k
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comparing strand-specific counts to unstranded counts
rnaseq strand deseq2
6.6 years ago lirongrossmann ▴ 80
0
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1
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2.4k
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Comment: C: Quantile normalization and Deseq2
6.6 years ago lirongrossmann ▴ 80
0
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3
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2.4k
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Quantile normalization and Deseq2
quantile normalization deseq2
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 80
12
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1
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7.2k
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identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 80
1
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4
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1.7k
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expression matrix with varianceStabilizingTransformation
deseq2 variancestabilizingtransformation rnaseq
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 80
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1
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1.7k
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Comment: C: expression matrix with varianceStabilizingTransformation
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 80
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0
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1.7k
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Comment: C: expression matrix with varianceStabilizingTransformation
6.6 years ago lirongrossmann ▴ 80
0
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1
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1.3k
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Comment: C: differential splicing events and covariates
6.6 years ago lirongrossmann ▴ 80
0
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3
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1.3k
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differential splicing events and covariates
limma rna-seq alternative splicing
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 80
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0
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3.2k
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Comment: C: Different PCA plots using rlog and vsd on the same data set
6.6 years ago lirongrossmann ▴ 80
0
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0
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2.4k
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Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
6.6 years ago lirongrossmann ▴ 80
0
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0
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2.4k
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Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
6.6 years ago lirongrossmann ▴ 80
0
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4
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2.4k
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RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
rangedsummarizedexperiment deseqdatasetfrommatrix deseq2 tximport
6.6 years ago lirongrossmann ▴ 80
0
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0
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3.2k
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Comment: A: Different PCA plots using rlog and vsd on the same data set
6.6 years ago lirongrossmann ▴ 80
0
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6
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3.2k
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Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.7 years ago • updated 6.6 years ago lirongrossmann ▴ 80
0
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5
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2.5k
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Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
6.7 years ago • updated 6.6 years ago lirongrossmann ▴ 80
0
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1
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2.5k
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Comment: A: Choosing genes for clustering
6.6 years ago lirongrossmann ▴ 80
0
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1
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3.2k
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Comment: A: Different PCA plots using rlog and vsd on the same data set
6.6 years ago lirongrossmann ▴ 80
0
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1
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1.5k
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Comment: C: Selecting genes that best separate between two groups
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 80
1
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3
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1.5k
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Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.7 years ago lirongrossmann ▴ 80
0
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0
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2.5k
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Comment: A: Choosing genes for clustering
6.7 years ago lirongrossmann ▴ 80
0
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0
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906
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
6.7 years ago lirongrossmann ▴ 80
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