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Comment: Comment: differential loop using DESeq2
4.1 years ago ATpoint ★ 4.7k
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Comment: Comment: Failed to find a rowRanges() method
4.1 years ago ATpoint ★ 4.7k
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Answer: Answer: Failed to find a rowRanges() method
4.1 years ago ATpoint ★ 4.7k
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Answer: Comment: Using Deseq2 for RNA-seq analysis of 4 different groups of cells
4.1 years ago ATpoint ★ 4.7k
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Comment: Comment: Using transformed matrix in DESeq2
4.1 years ago ATpoint ★ 4.7k
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Comment: Comment: Extract canonical coding sequence with getBM
4.1 years ago ATpoint ★ 4.7k
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Answer: Comment: Using transformed matrix in DESeq2
4.1 years ago ATpoint ★ 4.7k
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Comment: Comment: Extract canonical coding sequence with getBM
4.1 years ago ATpoint ★ 4.7k
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Answer: Comment: DESeq2 interactions genotype condition code needed
4.1 years ago ATpoint ★ 4.7k
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Answer: Comment: Trouble with Tximport
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: Differential expression on RNAseq without replicates
4.2 years ago ATpoint ★ 4.7k
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Comment: Answer: Recycling a DNAStringSet over an IRangesList in extractAt()
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: DESEQ2 Differential Expression controlling for two factors
4.2 years ago ATpoint ★ 4.7k
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Answer: Answer: DESeq2 variance stabilizing transformation: why is assay() different from getVar
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: Normalization in DiffBind for Atac-seq
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: Normalization in DiffBind for Atac-seq
4.2 years ago ATpoint ★ 4.7k
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Answer: Answer: Add selected row names on pheatmap
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: How well does "Trinity-Differential-Expression" work on normalized raw counts wi
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: to extract the mRNA sequences of the canonical RefSeq genes
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: WHat is the difference between DEG and TopVarGenes in DESEq2?
4.2 years ago ATpoint ★ 4.7k
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Answer: Answer: WHat is the difference between DEG and TopVarGenes in DESEq2?
4.2 years ago ATpoint ★ 4.7k
5
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Answer: Comment: Normalise to a housekeeping gene in DESEq2
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: Different contrast coding strategies in DESeq2 produce slightly different output
4.2 years ago ATpoint ★ 4.7k
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Answer: Comment: Bioconductor install error
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: Analyzing publicly available DESeq2 normalized counts for differential expressio
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be
4.2 years ago ATpoint ★ 4.7k
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Comment: Comment: HELP! Troubleshooting Installing EBImage Package
4.3 years ago ATpoint ★ 4.7k
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Comment: Comment: se does not inherit from class SummarizedExperiment
4.3 years ago ATpoint ★ 4.7k
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1.9k
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Comment: Comment: How to shortlist the unaffected gene list from DESeq2 results
4.3 years ago ATpoint ★ 4.7k
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catchSalmon for tx-level DE
catchSalmon edgeR
updated 15 months ago by 52k • written 4.3 years ago by ★ 4.7k
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Comment: Comment: catchSalmon for tx-level DE
4.3 years ago ATpoint ★ 4.7k
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Comment: C: DiffBind for ATACseq without replicates
4.3 years ago ATpoint ★ 4.7k
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edgeR for single-cell data with inferential replicates
edgeR alevin
4.3 years ago ATpoint ★ 4.7k
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Comment: C: Correctly set contrast with DESeq2 for not full rank design matrix
4.3 years ago ATpoint ★ 4.7k
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Comment: C: csaw for ATAC, quantitation of Tn5 insertion sites only
4.3 years ago ATpoint ★ 4.7k
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Comment: C: edgeR for single-cell data with inferential replicates
4.3 years ago ATpoint ★ 4.7k
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Comment: C: DESeq2::rlogTransformation missing rownames vs vst.
4.4 years ago ATpoint ★ 4.7k
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Comment: C: Contrasts in DESeq2
4.4 years ago ATpoint ★ 4.7k
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Comment: C: Contrasts in DESeq2
4.4 years ago ATpoint ★ 4.7k
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Comment: C: DESeq2 # of up-and down-regulated genes are approximately equal
4.4 years ago ATpoint ★ 4.7k
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Answer: C: padj NA after shrinking log2FC (DESeq2)
4.4 years ago ATpoint ★ 4.7k
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805
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Answer: C: Limma Design Matrix Missing Columns
4.4 years ago ATpoint ★ 4.7k
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1
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Comment: C: RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
4.4 years ago ATpoint ★ 4.7k
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Comment: C: RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
4.4 years ago ATpoint ★ 4.7k
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Comment: C: How to use GOseq without length bias
4.4 years ago ATpoint ★ 4.7k
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2.9k
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Comment: C: How to use GOseq without length bias
4.4 years ago ATpoint ★ 4.7k
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Comment: C: edgeR and batch effects
4.4 years ago ATpoint ★ 4.7k
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1.2k
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Comment: C: edgeR and batch effects
4.4 years ago ATpoint ★ 4.7k
2
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1
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1.5k
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normOffsets in csaw
csaw
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ★ 4.7k
2
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3
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1.4k
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vst with output of edgeR::calcNormFactors
DESeq2
updated 2.3 years ago by 52k • written 4.4 years ago by ★ 4.7k
1,022 results • Page 19 of 21
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