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Answer: Answer: Specifying design in DESeqDataSetFromMatrix
19 months ago ATpoint ★ 4.6k
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Answer: Answer: package is not available for this version of R
19 months ago ATpoint ★ 4.6k
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Answer: Answer: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago ATpoint ★ 4.6k
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Comment: Comment: Identify highly variable genes after vst
19 months ago ATpoint ★ 4.6k
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Answer: Answer: Identify highly variable genes after vst
19 months ago ATpoint ★ 4.6k
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Comment: Comment: how to remove batch effects of RNA seq data based on continuous variables(like s
19 months ago ATpoint ★ 4.6k
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Comment: Comment: PCA for QC should include subset of top variable genes or full set of genes in R
19 months ago ATpoint ★ 4.6k
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Answer: Answer: Error in SingleR, no common genes between 'test' and 'ref'
19 months ago ATpoint ★ 4.6k
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Comment: Comment: DESeq2 design formula
19 months ago ATpoint ★ 4.6k
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827
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Answer: Answer: really low padj value from DESeq2
19 months ago ATpoint ★ 4.6k
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Answer: Answer: PCA for QC should include subset of top variable genes or full set of genes in R
19 months ago ATpoint ★ 4.6k
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904
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Comment: Comment: Normalization of different input materials
19 months ago ATpoint ★ 4.6k
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851
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Answer: Answer: DESEQ2 differential expression for subsets of data?
19 months ago ATpoint ★ 4.6k
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2.4k
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Comment: Comment: Choosing between VST and rlog for PCA for outlier identification in DESeq2 when
19 months ago ATpoint ★ 4.6k
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758
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Answer: Answer: plotCounts label each sample
19 months ago ATpoint ★ 4.6k
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2.4k
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Comment: Comment: Choosing between VST and rlog for PCA for outlier identification in DESeq2 when
19 months ago ATpoint ★ 4.6k
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1.5k
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Answer: Answer: What GENCODE GFF file for calculating exon length for TPM
19 months ago ATpoint ★ 4.6k
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Comment: Comment: fastMNN reproducibility across machines when using Docker
19 months ago ATpoint ★ 4.6k
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904
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Answer: Answer: Normalization of different input materials
19 months ago ATpoint ★ 4.6k
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738
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Answer: Answer: WGCNA Cluster batch effect
19 months ago ATpoint ★ 4.6k
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1.5k
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Comment: Comment: DESeq2 package unrecognized after downloading latest version of R: keep getting
19 months ago ATpoint ★ 4.6k
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1
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853
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Answer: Answer: limma paired design
19 months ago ATpoint ★ 4.6k
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Answer: Answer: runPCA in a SingleCellExperiment results ina colMeans error
19 months ago ATpoint ★ 4.6k
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1.1k
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Answer: Answer: Hub genes selection in WGCNA
19 months ago ATpoint ★ 4.6k
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1.1k
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Comment: Comment: 'Killed' error during RNAseq alignment
19 months ago ATpoint ★ 4.6k
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1.1k
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Comment: Comment: Get Intron Seq
19 months ago ATpoint ★ 4.6k
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1.5k
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Answer: Answer: DESeq2 package unrecognized after downloading latest version of R: keep getting
19 months ago ATpoint ★ 4.6k
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1.2k
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Comment: Comment: DESeq2 with nbinomGLM issues
19 months ago ATpoint ★ 4.6k
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785
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Comment: Comment: RNA seq differential expression analysis
20 months ago ATpoint ★ 4.6k
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10k
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Answer: Answer: scran ScoreMarkers throws a warning
20 months ago ATpoint ★ 4.6k
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2
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976
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Answer: Answer: tximport error in reading salmon output files?
20 months ago ATpoint ★ 4.6k
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3.8k
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Answer: Answer: Making MDS plot
20 months ago ATpoint ★ 4.6k
2
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2
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1.3k
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Answer: Answer: DESeq2 lfcShrink function used in DiffBind package
20 months ago ATpoint ★ 4.6k
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1
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1.4k
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Answer: Answer: Fishpond/Swish Interaction Test Error
20 months ago ATpoint ★ 4.6k
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806
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Comment: Comment: Can DESeq2 handle low number of samples and replicates?
20 months ago ATpoint ★ 4.6k
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2.6k
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Answer: Answer: Whether to build DESeq2 model with all data and then contrast groups or subset g
20 months ago ATpoint ★ 4.6k
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807
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Answer: Answer: mia package installation has non-zero exit status
20 months ago ATpoint ★ 4.6k
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615
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Answer: Answer: DESeq2 how to extract expression values corresponding to log2FoldChange
20 months ago ATpoint ★ 4.6k
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1.6k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
20 months ago ATpoint ★ 4.6k
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1
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1.6k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
20 months ago ATpoint ★ 4.6k
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770
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Answer: Answer: Individual DESeq2 runs versus a single DESeq2 run with contrasts produce differe
20 months ago ATpoint ★ 4.6k
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481
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Answer: Answer: Several questions about the workflow using DESeq2 to process RNA data
20 months ago ATpoint ★ 4.6k
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1.8k
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Comment: Comment: P-value histogram of testLinearModel is not uniform
20 months ago ATpoint ★ 4.6k
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1.1k
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Answer: Answer: DESeq2 on multilevel design variable
20 months ago ATpoint ★ 4.6k
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1.1k
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Comment: Comment: Extract Limma Adjusted Values for Plotting
20 months ago ATpoint ★ 4.6k
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1.8k
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Answer: Answer: Handling NA's in Deseq2
20 months ago ATpoint ★ 4.6k
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1.1k
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Answer: Answer: Remove duplicate genera in DEseq output?
20 months ago ATpoint ★ 4.6k
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1.0k
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Comment: Comment: Recount3: PCR duplicates
20 months ago ATpoint ★ 4.6k
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835
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Answer: Answer: Normalized counts from LRT or Wald test?
20 months ago ATpoint ★ 4.6k
2
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760
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Answer: Answer: DESeq2 or edgeR for Presence and Absence of Proteins
20 months ago ATpoint ★ 4.6k
1,017 results • Page 8 of 21
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