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Comment: Comment: Failed to find a rowRanges() method
3.7 years ago ATpoint ★ 4.4k
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1
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3.3k
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Answer: Answer: Failed to find a rowRanges() method
3.7 years ago ATpoint ★ 4.4k
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0
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504
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Answer: Comment: Using Deseq2 for RNA-seq analysis of 4 different groups of cells
3.7 years ago ATpoint ★ 4.4k
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1.3k
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Comment: Comment: Using transformed matrix in DESeq2
3.7 years ago ATpoint ★ 4.4k
0
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1
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2.4k
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Comment: Comment: Extract canonical coding sequence with getBM
3.7 years ago ATpoint ★ 4.4k
0
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1
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1.3k
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Answer: Comment: Using transformed matrix in DESeq2
3.7 years ago ATpoint ★ 4.4k
0
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1
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2.4k
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Comment: Comment: Extract canonical coding sequence with getBM
3.8 years ago ATpoint ★ 4.4k
1
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0
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866
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Answer: Comment: DESeq2 interactions genotype condition code needed
3.8 years ago ATpoint ★ 4.4k
0
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0
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1.3k
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Answer: Comment: Trouble with Tximport
3.8 years ago ATpoint ★ 4.4k
0
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0
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1.0k
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Comment: Comment: Differential expression on RNAseq without replicates
3.8 years ago ATpoint ★ 4.4k
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0
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1.2k
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Comment: Answer: Recycling a DNAStringSet over an IRangesList in extractAt()
3.8 years ago ATpoint ★ 4.4k
0
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0
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679
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Comment: Comment: DESEQ2 Differential Expression controlling for two factors
3.8 years ago ATpoint ★ 4.4k
3
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1
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1.6k
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Answer: Answer: DESeq2 variance stabilizing transformation: why is assay() different from getVar
3.8 years ago ATpoint ★ 4.4k
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2
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3.0k
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Comment: Comment: Normalization in DiffBind for Atac-seq
3.8 years ago ATpoint ★ 4.4k
0
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1
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3.0k
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Comment: Comment: Normalization in DiffBind for Atac-seq
3.8 years ago ATpoint ★ 4.4k
0
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0
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8.7k
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Answer: Answer: Add selected row names on pheatmap
3.8 years ago ATpoint ★ 4.4k
0
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1
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1.6k
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Comment: Comment: How well does "Trinity-Differential-Expression" work on normalized raw counts wi
3.8 years ago ATpoint ★ 4.4k
1
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0
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1.9k
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Comment: Comment: to extract the mRNA sequences of the canonical RefSeq genes
3.8 years ago ATpoint ★ 4.4k
1
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0
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3.9k
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Comment: Comment: WHat is the difference between DEG and TopVarGenes in DESEq2?
3.8 years ago ATpoint ★ 4.4k
5
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1
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3.9k
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Answer: Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
3.8 years ago ATpoint ★ 4.4k
5
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1
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4.0k
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Answer: Comment: Normalise to a housekeeping gene in DESEq2
3.8 years ago ATpoint ★ 4.4k
1
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2
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1.5k
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Comment: Comment: Different contrast coding strategies in DESeq2 produce slightly different output
3.8 years ago ATpoint ★ 4.4k
1
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1
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2.6k
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Answer: Comment: Bioconductor install error
3.9 years ago ATpoint ★ 4.4k
0
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0
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1.2k
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Comment: Comment: Analyzing publicly available DESeq2 normalized counts for differential expressio
3.9 years ago ATpoint ★ 4.4k
0
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0
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3.2k
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Comment: Comment: Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be
3.9 years ago ATpoint ★ 4.4k
1
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1
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2.1k
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Comment: Comment: HELP! Troubleshooting Installing EBImage Package
3.9 years ago ATpoint ★ 4.4k
0
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0
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1.2k
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Comment: Comment: se does not inherit from class SummarizedExperiment
3.9 years ago ATpoint ★ 4.4k
1
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1
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1.8k
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Comment: Comment: How to shortlist the unaffected gene list from DESeq2 results
3.9 years ago ATpoint ★ 4.4k
4
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3
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2.0k
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catchSalmon for tx-level DE
catchSalmon edgeR
updated 10 months ago by 51k • written 3.9 years ago by ★ 4.4k
0
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1
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2.0k
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Comment: Comment: catchSalmon for tx-level DE
3.9 years ago ATpoint ★ 4.4k
0
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1
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2.8k
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Comment: C: DiffBind for ATACseq without replicates
3.9 years ago ATpoint ★ 4.4k
0
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2
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1.5k
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edgeR for single-cell data with inferential replicates
edgeR alevin
4.0 years ago ATpoint ★ 4.4k
0
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0
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1.5k
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Comment: C: Correctly set contrast with DESeq2 for not full rank design matrix
4.0 years ago ATpoint ★ 4.4k
0
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1
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2.9k
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Comment: C: csaw for ATAC, quantitation of Tn5 insertion sites only
4.0 years ago ATpoint ★ 4.4k
0
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0
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1.5k
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Comment: C: edgeR for single-cell data with inferential replicates
4.0 years ago ATpoint ★ 4.4k
1
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1
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1.3k
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Comment: C: DESeq2::rlogTransformation missing rownames vs vst.
4.0 years ago ATpoint ★ 4.4k
4
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1
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16k
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Comment: C: Contrasts in DESeq2
4.0 years ago ATpoint ★ 4.4k
1
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1
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16k
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Comment: C: Contrasts in DESeq2
4.0 years ago ATpoint ★ 4.4k
0
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0
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1.2k
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Comment: C: DESeq2 # of up-and down-regulated genes are approximately equal
4.0 years ago ATpoint ★ 4.4k
1
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0
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1.0k
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Answer: C: padj NA after shrinking log2FC (DESeq2)
4.0 years ago ATpoint ★ 4.4k
0
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0
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714
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Answer: C: Limma Design Matrix Missing Columns
4.0 years ago ATpoint ★ 4.4k
0
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1
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1.8k
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Comment: C: RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
4.0 years ago ATpoint ★ 4.4k
0
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1
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1.8k
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Comment: C: RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
4.0 years ago ATpoint ★ 4.4k
0
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0
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2.8k
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Comment: C: How to use GOseq without length bias
4.0 years ago ATpoint ★ 4.4k
0
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1
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2.8k
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Comment: C: How to use GOseq without length bias
4.0 years ago ATpoint ★ 4.4k
0
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0
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1.1k
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Comment: C: edgeR and batch effects
4.0 years ago ATpoint ★ 4.4k
1
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0
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1.1k
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Comment: C: edgeR and batch effects
4.0 years ago ATpoint ★ 4.4k
2
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1
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1.4k
views
normOffsets in csaw
csaw
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ★ 4.4k
2
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3
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1.3k
views
vst with output of edgeR::calcNormFactors
DESeq2
updated 23 months ago by 51k • written 4.1 years ago by ★ 4.4k
0
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0
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1.3k
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Comment: C: vst with output of edgeR::calcNormFactors
4.1 years ago ATpoint ★ 4.4k
971 results • Page 18 of 20
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