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Answer: Answer: Pre-Filtering and Independent Filtering DESeq2
9 months ago by Michael Love ★ 2.6k
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2.1k
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Answer: Answer: error with Tximport when txOut = TRUE
9 months ago by Michael Love ★ 2.6k
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2.4k
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Answer: Answer: DESeq2 shrinking log fold-change
2.2 years ago by Michael Love ★ 2.6k
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1.6k
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Answer: Answer: DESeq2/Differential expression analysis without replicates
2.2 years ago by Michael Love ★ 2.6k
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1.1k
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Answer: Answer: Is there a minimum read count or number of genes for Salmon bias correction?
2.2 years ago by Michael Love ★ 2.6k
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876
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Answer: Answer: fishpond RNA-seq analysis: Two genotype and four treatments
2.3 years ago by Michael Love ★ 2.6k
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1.2k
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Answer: Answer: salmon quantification and then generating BAM files using STAR
2.3 years ago by Michael Love ★ 2.6k
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1.1k
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Answer: Answer: Mendelian Randomisation with GTEx data
2.3 years ago by Michael Love ★ 2.6k
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1.2k
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Answer: Answer: DEG analysis from Salmon quantification of 3' TagSeq reads with unannotated refe
2.3 years ago by Michael Love ★ 2.6k
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2.0k
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Answer: Answer: how to understand the P value of the Deseq2 results
3.0 years ago by Michael Love ★ 2.6k
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2.1k
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Answer: A: DESEq2 error - 'DESeqDataSet' object superclass 'RectangularData' not defined in
3.2 years ago by Michael Love ★ 2.6k
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2.9k
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Answer: C: How is the bootstrapping information from kallisto treated in DeSeq2 when import
3.6 years ago by Michael Love ★ 2.6k
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1
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4.0k
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Answer: A: DESeq2 analysis with covariates with and without log transformation
3.8 years ago by Michael Love ★ 2.6k
7
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5.7k
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Answer: A: How to import RSEM results to DESeq2 for differential analysis
updated 4.2 years ago by 82k • written 6.4 years ago by ★ 2.6k
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9.9k
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Answer: C: Is a simple Wilcoxon rank sum test good enough to identify differentially expres
4.2 years ago by Michael Love ★ 2.6k
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1
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8.8k
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Answer: A: To What Degree Could We Determine Whether A Gene Is Expressed?
updated 4.4 years ago by 43k • written 10.0 years ago by ★ 2.6k
3
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2
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Answer: Answer: Is inspection and correction of pvalues still needed in DESeq2?
updated 17 months ago by 43k • written 8.8 years ago by ★ 2.6k
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2
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8.1k
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Answer: A: "Duplicate rownames not allowed" when the rownames are not duplicated
5.6 years ago by Michael Love ★ 2.6k
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2.7k
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Answer: A: what's the meaning of a Concordance at the Top plot(CAT plot)
6.5 years ago by Michael Love ★ 2.6k
7
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26k
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Answer: A: Gene Set Enrichment Analysis after DESeq2
6.5 years ago by Michael Love ★ 2.6k
3
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1
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2.8k
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Answer: A: Efficient way to run a DESeq2 analysis with many design formulae
6.7 years ago by Michael Love ★ 2.6k
2
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1
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5.0k
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Answer: A: Why DESeq2 in parallel mode is slower than normal?!
6.9 years ago by Michael Love ★ 2.6k
2
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4.0k
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Answer: A: How to define a non differentially expressed gene?
7.1 years ago by Michael Love ★ 2.6k
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4.5k
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Answer: A: DESeq2 - how to build design for multiple paired samples before/after with 2 con
7.2 years ago by Michael Love ★ 2.6k
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3.2k
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Answer: A: DESeqDataSetFromMatrix Error in if/while (condition) {: missing Value where TRUE
7.4 years ago by Michael Love ★ 2.6k
3
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1
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1.6k
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Answer: C: Coping with a label imbalance in DESeq2
7.6 years ago by Michael Love ★ 2.6k
3
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1
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45k
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Answer: A: Up-to-date RNA-Seq Analysis Training/Courses/Papers (July 2016)
7.8 years ago by Michael Love ★ 2.6k
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2.6k
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Answer: A: The best test for the two conditional problem.
8.0 years ago by Michael Love ★ 2.6k
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3.3k
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Answer: A: clustering from breast cancer RNA-seq data
8.0 years ago by Michael Love ★ 2.6k
2
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0
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8.7k
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Answer: A: Time course experiments in DESeq2
8.0 years ago by Michael Love ★ 2.6k
2
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1
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5.1k
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Answer: A: Using 'tximport' library for downstream DGE after quantifying with Kallisto
8.0 years ago by Michael Love ★ 2.6k
18
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1
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36k
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Answer: A: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
8.1 years ago by Michael Love ★ 2.6k
2
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1
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8.2k
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Answer: A: following Kallisto with DESeq2 using tximport package
8.2 years ago by Michael Love ★ 2.6k
1
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4.7k
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Answer: A: Shrinking fold change and dispersion for RNA-seq data ( DESeq2)
8.6 years ago by Michael Love ★ 2.6k
5
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0
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4.8k
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Answer: A: Why is DESeq a better method for finding highly upregulated and downregulated ge
8.8 years ago by Michael Love ★ 2.6k
1
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1
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13k
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Answer: A: Deseq2 gene name annotation
8.8 years ago by Michael Love ★ 2.6k
1
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2.7k
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Answer: A: Running DESeqDataSet with 4 factors?
8.8 years ago by Michael Love ★ 2.6k
0
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0
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4.5k
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Answer: Answer: Deseq web-based (with GUI)
updated 17 months ago by 43k • written 8.8 years ago by ★ 2.6k
3
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1
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9.8k
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Answer: Answer: How to remove batch effect from RNA-seq data?
updated 17 months ago by 43k • written 8.8 years ago by ★ 2.6k
5
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0
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4.9k
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Answer: A: DESeq2: different log2FC results when using subset of data
8.8 years ago by Michael Love ★ 2.6k
2
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1.5k
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Answer: A: Summarized Experiment _normrange
8.8 years ago by Michael Love ★ 2.6k
4
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0
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12k
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Answer: Answer: DESeq2 - "all gene-wise dispersion estimates are within 2 orders of magnitude"
updated 17 months ago by 43k • written 8.8 years ago by ★ 2.6k
4
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1
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7.6k
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Answer: Answer: DESeq2 analysis: huge number of outliers and refitting
updated 17 months ago by 43k • written 8.8 years ago by ★ 2.6k
6
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1
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11k
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Answer: Answer: fold change vs standardized effect size
updated 15 months ago by 43k • written 9.0 years ago by ★ 2.6k
1
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2
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3.0k
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Answer: Answer: DESeq2 - Warning message
updated 15 months ago by 43k • written 9.0 years ago by ★ 2.6k
1
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1
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3.3k
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Answer: A: DESeq2 with 2 factors: problem to fit the negative binomial and weird p-value di
9.0 years ago by Michael Love ★ 2.6k
2
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1
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12k
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Answer: A: DESeq2 normalisation: is the size of the gene taken into account?
9.0 years ago by Michael Love ★ 2.6k
1
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1
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3.8k
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Answer: Answer: DESeq2: invalid class “GRangesList” object
updated 24 months ago by 43k • written 9.2 years ago by ★ 2.6k
2
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1
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4.2k
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Answer: Answer: [DESeq2] Little Error in seq_len(nrow(modelMatrix)) while starting DESeq()
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 2.6k
36
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0
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22k
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Answer: Answer: Can someone please explain in simple terms how DESeq2 works?
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 2.6k
62 results • Page 1 of 2
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