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Comment: Comment: Reading data into chromVAR
14 months ago ATpoint ★ 4.4k
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Comment: Comment: Pairwise comparison for DEG analysis
14 months ago ATpoint ★ 4.4k
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Answer: Answer: DGE analysis for diseased samples through DESeq2 and Ballgown
14 months ago ATpoint ★ 4.4k
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Comment: Comment: lfc direction of effect flipped for ashr, apeGLM, but accurate to biological dat
14 months ago ATpoint ★ 4.4k
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Answer: Answer: Specifying design in DESeqDataSetFromMatrix
14 months ago ATpoint ★ 4.4k
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Answer: Answer: package is not available for this version of R
14 months ago ATpoint ★ 4.4k
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Answer: Answer: Importing RSEM processed data already formatted as a summarized experiment into
15 months ago ATpoint ★ 4.4k
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Comment: Comment: Identify highly variable genes after vst
15 months ago ATpoint ★ 4.4k
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Answer: Answer: Identify highly variable genes after vst
15 months ago ATpoint ★ 4.4k
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Comment: Comment: how to remove batch effects of RNA seq data based on continuous variables(like s
15 months ago ATpoint ★ 4.4k
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Comment: Comment: PCA for QC should include subset of top variable genes or full set of genes in R
15 months ago ATpoint ★ 4.4k
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1.3k
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Answer: Answer: Error in SingleR, no common genes between 'test' and 'ref'
15 months ago ATpoint ★ 4.4k
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Comment: Comment: DESeq2 design formula
15 months ago ATpoint ★ 4.4k
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Answer: Answer: really low padj value from DESeq2
15 months ago ATpoint ★ 4.4k
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Answer: Answer: PCA for QC should include subset of top variable genes or full set of genes in R
15 months ago ATpoint ★ 4.4k
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779
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Comment: Comment: Normalization of different input materials
15 months ago ATpoint ★ 4.4k
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760
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Answer: Answer: DESEQ2 differential expression for subsets of data?
15 months ago ATpoint ★ 4.4k
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1.9k
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Comment: Comment: Choosing between VST and rlog for PCA for outlier identification in DESeq2 when
15 months ago ATpoint ★ 4.4k
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641
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Answer: Answer: plotCounts label each sample
15 months ago ATpoint ★ 4.4k
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1.9k
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Comment: Comment: Choosing between VST and rlog for PCA for outlier identification in DESeq2 when
15 months ago ATpoint ★ 4.4k
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1.2k
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Answer: Answer: What GENCODE GFF file for calculating exon length for TPM
15 months ago ATpoint ★ 4.4k
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913
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Comment: Comment: fastMNN reproducibility across machines when using Docker
15 months ago ATpoint ★ 4.4k
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779
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Answer: Answer: Normalization of different input materials
15 months ago ATpoint ★ 4.4k
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650
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Answer: Answer: WGCNA Cluster batch effect
15 months ago ATpoint ★ 4.4k
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993
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Comment: Comment: DESeq2 package unrecognized after downloading latest version of R: keep getting
15 months ago ATpoint ★ 4.4k
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779
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Answer: Answer: limma paired design
15 months ago ATpoint ★ 4.4k
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Answer: Answer: runPCA in a SingleCellExperiment results ina colMeans error
15 months ago ATpoint ★ 4.4k
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845
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Answer: Answer: Hub genes selection in WGCNA
15 months ago ATpoint ★ 4.4k
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889
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Comment: Comment: 'Killed' error during RNAseq alignment
15 months ago ATpoint ★ 4.4k
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934
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Comment: Comment: Get Intron Seq
15 months ago ATpoint ★ 4.4k
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993
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Answer: Answer: DESeq2 package unrecognized after downloading latest version of R: keep getting
15 months ago ATpoint ★ 4.4k
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Comment: Comment: DESeq2 with nbinomGLM issues
15 months ago ATpoint ★ 4.4k
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Comment: Comment: RNA seq differential expression analysis
15 months ago ATpoint ★ 4.4k
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8.5k
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Answer: Answer: scran ScoreMarkers throws a warning
15 months ago ATpoint ★ 4.4k
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855
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Answer: Answer: tximport error in reading salmon output files?
15 months ago ATpoint ★ 4.4k
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2.9k
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Answer: Answer: Making MDS plot
15 months ago ATpoint ★ 4.4k
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1.1k
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Answer: Answer: DESeq2 lfcShrink function used in DiffBind package
15 months ago ATpoint ★ 4.4k
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Answer: Answer: Fishpond/Swish Interaction Test Error
15 months ago ATpoint ★ 4.4k
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666
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Comment: Comment: Can DESeq2 handle low number of samples and replicates?
15 months ago ATpoint ★ 4.4k
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2.0k
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Answer: Answer: Whether to build DESeq2 model with all data and then contrast groups or subset g
15 months ago ATpoint ★ 4.4k
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721
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Answer: Answer: mia package installation has non-zero exit status
15 months ago ATpoint ★ 4.4k
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545
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Answer: Answer: DESeq2 how to extract expression values corresponding to log2FoldChange
15 months ago ATpoint ★ 4.4k
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1.4k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
15 months ago ATpoint ★ 4.4k
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1.4k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
15 months ago ATpoint ★ 4.4k
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687
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Answer: Answer: Individual DESeq2 runs versus a single DESeq2 run with contrasts produce differe
15 months ago ATpoint ★ 4.4k
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434
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Answer: Answer: Several questions about the workflow using DESeq2 to process RNA data
15 months ago ATpoint ★ 4.4k
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Comment: Comment: P-value histogram of testLinearModel is not uniform
15 months ago ATpoint ★ 4.4k
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895
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Answer: Answer: DESeq2 on multilevel design variable
16 months ago ATpoint ★ 4.4k
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926
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Comment: Comment: Extract Limma Adjusted Values for Plotting
16 months ago ATpoint ★ 4.4k
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1.4k
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Answer: Answer: Handling NA's in Deseq2
16 months ago ATpoint ★ 4.4k
971 results • Page 7 of 20
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