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Comment: Comment: Choosing between VST and rlog for PCA for outlier identification in DESeq2 when
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: What GENCODE GFF file for calculating exon length for TPM
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: fastMNN reproducibility across machines when using Docker
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: Normalization of different input materials
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: WGCNA Cluster batch effect
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: DESeq2 package unrecognized after downloading latest version of R: keep getting
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: limma paired design
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: runPCA in a SingleCellExperiment results ina colMeans error
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: Hub genes selection in WGCNA
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: 'Killed' error during RNAseq alignment
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: Get Intron Seq
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: DESeq2 package unrecognized after downloading latest version of R: keep getting
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: DESeq2 with nbinomGLM issues
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: RNA seq differential expression analysis
2.5 years ago ATpoint ★ 5.0k
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11k
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Answer: Answer: scran ScoreMarkers throws a warning
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: tximport error in reading salmon output files?
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: Making MDS plot
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: DESeq2 lfcShrink function used in DiffBind package
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: Fishpond/Swish Interaction Test Error
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: Can DESeq2 handle low number of samples and replicates?
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: Whether to build DESeq2 model with all data and then contrast groups or subset g
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: mia package installation has non-zero exit status
2.5 years ago ATpoint ★ 5.0k
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738
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Answer: Answer: DESeq2 how to extract expression values corresponding to log2FoldChange
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
2.5 years ago ATpoint ★ 5.0k
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Answer: Answer: Individual DESeq2 runs versus a single DESeq2 run with contrasts produce differe
2.5 years ago ATpoint ★ 5.0k
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628
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Answer: Answer: Several questions about the workflow using DESeq2 to process RNA data
2.5 years ago ATpoint ★ 5.0k
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Comment: Comment: P-value histogram of testLinearModel is not uniform
2.5 years ago ATpoint ★ 5.0k
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1.4k
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Answer: Answer: DESeq2 on multilevel design variable
2.5 years ago ATpoint ★ 5.0k
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1.3k
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Comment: Comment: Extract Limma Adjusted Values for Plotting
2.5 years ago ATpoint ★ 5.0k
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2.3k
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Answer: Answer: Handling NA's in Deseq2
2.6 years ago ATpoint ★ 5.0k
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Answer: Answer: Remove duplicate genera in DEseq output?
2.6 years ago ATpoint ★ 5.0k
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Comment: Comment: Recount3: PCR duplicates
2.6 years ago ATpoint ★ 5.0k
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1.0k
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Answer: Answer: Normalized counts from LRT or Wald test?
2.6 years ago ATpoint ★ 5.0k
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899
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Answer: Answer: DESeq2 or edgeR for Presence and Absence of Proteins
2.6 years ago ATpoint ★ 5.0k
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Comment: Comment: Visualization of negative log CPM values
2.6 years ago ATpoint ★ 5.0k
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7.5k
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Comment: Comment: Visualization of negative log CPM values
2.6 years ago ATpoint ★ 5.0k
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Answer: Answer: DoparParam() execution fails when foreach() works
2.6 years ago ATpoint ★ 5.0k
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Answer: Answer: Nanostring data differential expression analysis: limma or DESeq2?
2.6 years ago ATpoint ★ 5.0k
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Answer: Answer: how to solve this error
2.6 years ago ATpoint ★ 5.0k
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1.9k
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Comment: Comment: How to update a package at Bioconductor
2.6 years ago ATpoint ★ 5.0k
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Comment: Comment: Installing densvis on a Singularity container
2.6 years ago ATpoint ★ 5.0k
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1.9k
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Answer: Answer: Subsetting DESeq data set to compare treatments within one group (multi-group ex
2.6 years ago ATpoint ★ 5.0k
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Comment: Comment: optimHess problem in apeglm/DESeq2
2.6 years ago ATpoint ★ 5.0k
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Answer: Answer: Docker usage with Trio Bioconductor Package
2.6 years ago ATpoint ★ 5.0k
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854
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Answer: Answer: How to determine if any samples are outliers in PCA? What is the criteria?
2.6 years ago ATpoint ★ 5.0k
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Comment: Comment: optimHess problem in apeglm/DESeq2
2.6 years ago ATpoint ★ 5.0k
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optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 2.6 years ago by 43k • written 2.6 years ago by ★ 5.0k
3
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Answer: Answer: 'Seurat' package
2.6 years ago ATpoint ★ 5.0k
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Answer: Answer: DESeq2: Comparison between 1 test sample with 1 control sample
2.6 years ago ATpoint ★ 5.0k
1,100 results • Page 10 of 22
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