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Comment: Comment: Is this featureCounts output normal, and how can I process it for DESeq2 analysi
11 months ago by Gordon Smyth ★ 8.4k
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Answer: Answer: Is this featureCounts output normal, and how can I process it for DESeq2 analysi
11 months ago by Gordon Smyth ★ 8.4k
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1.7k
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Comment: Comment: Handling Negative Values in Log-Transformed a Dataset for Differential Expressi
11 months ago by Gordon Smyth ★ 8.4k
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970
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Answer: Answer: Biostatistics
11 months ago by Gordon Smyth ★ 8.4k
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1.7k
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Comment: Comment: Handling Negative Values in Log-Transformed a Dataset for Differential Expressi
11 months ago by Gordon Smyth ★ 8.4k
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1.2k
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Answer: Answer: how to run limma for large datasets
11 months ago by Gordon Smyth ★ 8.4k
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1.4k
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Answer: Answer: [construct a model.matrix ]
11 months ago by Gordon Smyth ★ 8.4k
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1
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1.7k
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Answer: Answer: Handling Negative Values in Log-Transformed a Dataset for Differential Expressi
11 months ago by Gordon Smyth ★ 8.4k
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1.9k
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Answer: Answer: gene ID to gene symbol in R
12 months ago by Gordon Smyth ★ 8.4k
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1
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3.2k
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Comment: Comment: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
12 months ago by Gordon Smyth ★ 8.4k
3
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3.2k
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Answer: Answer: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
12 months ago by Gordon Smyth ★ 8.4k
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4.4k
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Answer: Answer: How does edgeR's filterByExpr work?
13 months ago by Gordon Smyth ★ 8.4k
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4.4k
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Comment: Comment: How does edgeR's filterByExpr work?
13 months ago by Gordon Smyth ★ 8.4k
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1
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2.8k
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Comment: Comment: Does the order of the batch variable matter in Limma design matrix?
13 months ago by Gordon Smyth ★ 8.4k
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2.4k
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Comment: Comment: Kallisto: to scaledTPM or not to scaledTPM
13 months ago by Gordon Smyth ★ 8.4k
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2.4k
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Comment: Comment: Kallisto: to scaledTPM or not to scaledTPM
13 months ago by Gordon Smyth ★ 8.4k
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2.4k
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Comment: Comment: Kallisto: to scaledTPM or not to scaledTPM
13 months ago by Gordon Smyth ★ 8.4k
1
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2.4k
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Answer: Answer: Kallisto: to scaledTPM or not to scaledTPM
13 months ago by Gordon Smyth ★ 8.4k
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0
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1.5k
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Comment: Comment: Seeking Advice on Using `edgeR` and `variancePartition` for RNA-seq Data with Mu
14 months ago by Gordon Smyth ★ 8.4k
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Comment: Comment: EdgeR gmlQLF with low number of genes
14 months ago by Gordon Smyth ★ 8.4k
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1.3k
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Answer: Answer: EdgeR gmlQLF with low number of genes
14 months ago by Gordon Smyth ★ 8.4k
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2.2k
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Comment: Comment: gene expression normaliztion
15 months ago by Gordon Smyth ★ 8.4k
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1.2k
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Answer: Answer: Bulk RNA seq analysis on multiple conditions (4)
updated 15 months ago by 45k • written 15 months ago by ★ 8.4k
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1.3k
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Comment: Comment: Pathway analysis for DGEList
15 months ago by Gordon Smyth ★ 8.4k
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1.5k
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Comment: Comment: Adjusting for covariates such as duration of diabetes, age, sex and BMI
16 months ago by Gordon Smyth ★ 8.4k
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1
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2.2k
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Answer: Answer: gene expression normaliztion
16 months ago by Gordon Smyth ★ 8.4k
3
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1
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952
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Answer: Answer: edgeR batch effect model matrix sanity check
16 months ago by Gordon Smyth ★ 8.4k
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769
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Comment: Comment: Design model matrix with limma with cell different proportions estimates and bat
16 months ago by Gordon Smyth ★ 8.4k
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3.1k
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Answer: Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
17 months ago by Gordon Smyth ★ 8.4k
2
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0
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761
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Answer: Answer: RNAseq coverage vs depth for transcript isoform expression?
17 months ago by Gordon Smyth ★ 8.4k
5
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1.0k
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Answer: Answer: EdgeR - relationship between logFC and coefficients
17 months ago by Gordon Smyth ★ 8.4k
1
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1
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1.4k
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Comment: Comment: Design matrix Differential expression analysis
18 months ago by Gordon Smyth ★ 8.4k
2
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1
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1.4k
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Answer: Answer: Design matrix Differential expression analysis
18 months ago by Gordon Smyth ★ 8.4k
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1
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1.4k
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Comment: Comment: Limma Analysis Agilent Microarray Data (GPL1708)
18 months ago by Gordon Smyth ★ 8.4k
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3.4k
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Answer: Answer: Differential Expression using Isoseq-supplemented reference transcriptome
18 months ago by Gordon Smyth ★ 8.4k
1
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1
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1.4k
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Answer: Answer: Limma Analysis Agilent Microarray Data (GPL1708)
18 months ago by Gordon Smyth ★ 8.4k
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1
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1.1k
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Answer: Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
18 months ago by Gordon Smyth ★ 8.4k
4
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1
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1.6k
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Answer: Answer: How to use limma to find differentially expressed genes in response to a continu
18 months ago by Gordon Smyth ★ 8.4k
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1.0k
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Comment: Comment: permutation test in edgeR
18 months ago by Gordon Smyth ★ 8.4k
1
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0
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950
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Comment: Comment: Difference when using difference number of pathways score to compare between 3 g
18 months ago by Gordon Smyth ★ 8.4k
1
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0
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787
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Answer: Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
18 months ago by Gordon Smyth ★ 8.4k
2
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1
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1.2k
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Answer: Answer: differential gene expression analysis when not all samples have an untreated cou
18 months ago by Gordon Smyth ★ 8.4k
1
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1
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1.1k
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Comment: Comment: Limma compare between 3 conditions vs 2 conditions
18 months ago by Gordon Smyth ★ 8.4k
2
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0
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841
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Answer: Answer: Choosing an FC Threshold
19 months ago by Gordon Smyth ★ 8.4k
1
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3.4k
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Comment: Comment: Shrink logFC values after edgeR
19 months ago by Gordon Smyth ★ 8.4k
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1
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2.0k
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Comment: Comment: 'Invalid parameter' error to generate a count matrix using featurecounts
19 months ago by Gordon Smyth ★ 8.4k
0
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1
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2.0k
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Answer: Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
19 months ago by Gordon Smyth ★ 8.4k
1
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0
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1.6k
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Comment: Comment: Differential express genes in imbalance groups
19 months ago by Gordon Smyth ★ 8.4k
3
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3
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1.6k
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Answer: Answer: Differential express genes in imbalance groups
19 months ago by Gordon Smyth ★ 8.4k
0
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0
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664
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Comment: Comment: Computing mid parent value for DE analysis
19 months ago by Gordon Smyth ★ 8.4k
586 results • Page 2 of 12
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