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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 80
1
vote
3
replies
1.3k
views
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
0
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0
replies
739
views
Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.7 years ago lirongrossmann ▴ 80
0
votes
1
reply
1.2k
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Handling outliers in Deseq2
outliers deseq2 logfoldchange
6.3 years ago lirongrossmann ▴ 80
9
votes
2
replies
5.3k
views
log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold deseq2
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 80
0
votes
1
reply
1.3k
views
Base mean count threshold
deseq2 base
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 80
1
vote
3
replies
3.1k
views
Batch effect removal with Deseq2
deseq2 batch effect removebatcheffect() limma
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 80
2
votes
2
replies
4.1k
views
choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 5 months ago by • 0 • written 6.4 years ago by ▴ 80
1
vote
2
replies
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
vote
1
reply
715
views
NA adjp with extremely low p value
deseq2 adjusted pvalue
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 80
0
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1
reply
1.2k
views
Distribution of transformed data using VST
variancestabilizingtransformation deseq2
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 80
0
votes
1
reply
477
views
Deseq2 for small matched samples
deseq2
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 80
2
votes
5
replies
1.5k
views
calculating logfold change from variance stabilizing transformation
deseq2 logfoldchange variancestabilizingtransformation
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 80
2
votes
8
replies
2.4k
views
comparing strand-specific counts to unstranded counts
rnaseq strand deseq2
6.5 years ago lirongrossmann ▴ 80
0
votes
3
replies
2.4k
views
Quantile normalization and Deseq2
quantile normalization deseq2
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 80
12
votes
1
reply
7.1k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 80
1
vote
4
replies
1.7k
views
expression matrix with varianceStabilizingTransformation
deseq2 variancestabilizingtransformation rnaseq
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 80
0
votes
3
replies
1.3k
views
differential splicing events and covariates
limma rna-seq alternative splicing
updated 6.5 years ago by 50k • written 6.5 years ago by ▴ 80
0
votes
4
replies
2.3k
views
RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
rangedsummarizedexperiment deseqdatasetfrommatrix deseq2 tximport
6.6 years ago lirongrossmann ▴ 80
0
votes
6
replies
3.1k
views
Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.6 years ago lirongrossmann ▴ 80
0
votes
5
replies
2.4k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
6.6 years ago lirongrossmann ▴ 80
1
vote
3
replies
1.5k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.6 years ago lirongrossmann ▴ 80
0
votes
0
replies
899
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
6.6 years ago lirongrossmann ▴ 80
11
votes
8
replies
10k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 80
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