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854
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Comment: C: Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
21 months ago lirongrossmann ▴ 60
0
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6
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854
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 60
0
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0
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854
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Comment: C: Cluster location in UMAP using SingleCellExperiment and SingleR
21 months ago lirongrossmann ▴ 60
0
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0
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438
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Comment: C: Raw counts for reference dataset in single cell rnaseq
21 months ago lirongrossmann ▴ 60
1
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3
replies
438
views
Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 60
0
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0
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497
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Comment: C: marker genes in single cell experiment
21 months ago lirongrossmann ▴ 60
0
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0
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516
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Comment: C: most correlated genes in SingleR
21 months ago lirongrossmann ▴ 60
0
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0
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282
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Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
21 months ago lirongrossmann ▴ 60
0
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0
replies
751
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Comment: C: Trajectory analysis for single cell sequencing
21 months ago lirongrossmann ▴ 60
0
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1
reply
751
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Comment: C: Trajectory analysis for single cell sequencing
21 months ago lirongrossmann ▴ 60
0
votes
1
reply
587
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Handling outliers in Deseq2
outliers deseq2 logfoldchange
4.4 years ago lirongrossmann ▴ 60
8
votes
2
replies
2.9k
views
log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold deseq2
updated 4.4 years ago by 37k • written 4.4 years ago by ▴ 60
0
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1
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962
views
Base mean count threshold
deseq2 base
updated 4.4 years ago by 37k • written 4.4 years ago by ▴ 60
0
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1
reply
2.3k
views
Comment: C: Batch effect removal with Deseq2
4.4 years ago lirongrossmann ▴ 60
1
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3
replies
2.3k
views
Batch effect removal with Deseq2
deseq2 batch effect removebatcheffect() limma
updated 4.4 years ago by 37k • written 4.4 years ago by ▴ 60
2
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1
reply
2.4k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 4.5 years ago by 37k • written 4.5 years ago by ▴ 60
0
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0
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917
views
Answer: A: an unexplained phenomenon using variance stabilizing transformation for downstre
4.5 years ago lirongrossmann ▴ 60
1
vote
2
replies
917
views
an unexplained phenomenon using variance stabilizing transformation for downstream analysis
variancestabilizingtransformation normalization
4.5 years ago lirongrossmann ▴ 60
1
vote
1
reply
481
views
NA adjp with extremely low p value
deseq2 adjusted pvalue
updated 4.5 years ago by 37k • written 4.5 years ago by ▴ 60
0
votes
1
reply
636
views
Distribution of transformed data using VST
variancestabilizingtransformation deseq2
updated 4.5 years ago by 37k • written 4.5 years ago by ▴ 60
0
votes
1
reply
375
views
Deseq2 for small matched samples
deseq2
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
0
votes
1
reply
778
views
Comment: C: calculating logfold change from variance stabilizing transformation
4.6 years ago lirongrossmann ▴ 60
0
votes
1
reply
778
views
Comment: C: calculating logfold change from variance stabilizing transformation
4.6 years ago lirongrossmann ▴ 60
2
votes
5
replies
778
views
calculating logfold change from variance stabilizing transformation
deseq2 logfoldchange variancestabilizingtransformation
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
0
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0
replies
1.1k
views
Comment: C: comparing strand-specific counts to unstranded counts
4.6 years ago lirongrossmann ▴ 60
0
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1
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1.1k
views
Comment: C: comparing strand-specific counts to unstranded counts
4.6 years ago lirongrossmann ▴ 60
0
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1
reply
1.1k
views
Comment: C: comparing strand-specific counts to unstranded counts
4.6 years ago lirongrossmann ▴ 60
2
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8
replies
1.1k
views
comparing strand-specific counts to unstranded counts
rnaseq strand deseq2
4.6 years ago lirongrossmann ▴ 60
0
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1
reply
1.1k
views
Comment: A: comparing strand-specific counts to unstranded counts
4.6 years ago lirongrossmann ▴ 60
0
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1
reply
1.6k
views
Comment: C: Quantile normalization and Deseq2
4.6 years ago lirongrossmann ▴ 60
0
votes
3
replies
1.6k
views
Quantile normalization and Deseq2
quantile normalization deseq2
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
11
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1
reply
4.7k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
1
vote
4
replies
901
views
expression matrix with varianceStabilizingTransformation
deseq2 variancestabilizingtransformation rnaseq
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
0
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1
reply
901
views
Comment: C: expression matrix with varianceStabilizingTransformation
updated 4.6 years ago by 37k • written 4.6 years ago by ▴ 60
0
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0
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901
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Comment: C: expression matrix with varianceStabilizingTransformation
4.6 years ago lirongrossmann ▴ 60
0
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1
reply
789
views
Comment: C: differential splicing events and covariates
4.6 years ago lirongrossmann ▴ 60
0
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3
replies
789
views
differential splicing events and covariates
limma rna-seq alternative splicing
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 60
0
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0
replies
1.5k
views
Comment: C: Different PCA plots using rlog and vsd on the same data set
4.7 years ago lirongrossmann ▴ 60
0
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0
replies
1.1k
views
Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
4.7 years ago lirongrossmann ▴ 60
0
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0
replies
1.1k
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Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
4.7 years ago lirongrossmann ▴ 60
0
votes
4
replies
1.1k
views
RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
rangedsummarizedexperiment deseqdatasetfrommatrix deseq2 tximport
4.7 years ago lirongrossmann ▴ 60
0
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0
replies
1.5k
views
Comment: A: Different PCA plots using rlog and vsd on the same data set
4.7 years ago lirongrossmann ▴ 60
0
votes
6
replies
1.5k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
4.7 years ago lirongrossmann ▴ 60
0
votes
5
replies
1.2k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
4.7 years ago lirongrossmann ▴ 60
0
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1
reply
1.2k
views
Comment: A: Choosing genes for clustering
4.7 years ago lirongrossmann ▴ 60
0
votes
1
reply
1.5k
views
Comment: A: Different PCA plots using rlog and vsd on the same data set
4.7 years ago lirongrossmann ▴ 60
0
votes
1
reply
765
views
Comment: C: Selecting genes that best separate between two groups
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 60
1
vote
3
replies
765
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
4.7 years ago lirongrossmann ▴ 60
0
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0
replies
1.2k
views
Comment: A: Choosing genes for clustering
4.7 years ago lirongrossmann ▴ 60
0
votes
0
replies
560
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
4.7 years ago lirongrossmann ▴ 60
56 results • Page 1 of 2
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