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Showing :
answers
1
vote
0
replies
1.1k
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Answer:
Answer: Pre-Filtering and Independent Filtering DESeq2
10 months ago by
Michael Love
★ 2.6k
1
vote
2
replies
2.1k
views
Answer:
Answer: error with Tximport when txOut = TRUE
10 months ago by
Michael Love
★ 2.6k
0
votes
1
reply
2.5k
views
Answer:
Answer: DESeq2 shrinking log fold-change
2.3 years ago by
Michael Love
★ 2.6k
0
votes
1
reply
1.6k
views
Answer:
Answer: DESeq2/Differential expression analysis without replicates
2.3 years ago by
Michael Love
★ 2.6k
6
votes
1
reply
1.2k
views
Answer:
Answer: Is there a minimum read count or number of genes for Salmon bias correction?
2.3 years ago by
Michael Love
★ 2.6k
1
vote
1
reply
893
views
Answer:
Answer: fishpond RNA-seq analysis: Two genotype and four treatments
2.3 years ago by
Michael Love
★ 2.6k
2
votes
0
replies
1.2k
views
Answer:
Answer: salmon quantification and then generating BAM files using STAR
2.3 years ago by
Michael Love
★ 2.6k
0
votes
0
replies
1.1k
views
Answer:
Answer: Mendelian Randomisation with GTEx data
2.3 years ago by
Michael Love
★ 2.6k
4
votes
0
replies
1.2k
views
Answer:
Answer: DEG analysis from Salmon quantification of 3' TagSeq reads with unannotated refe
2.4 years ago by
Michael Love
★ 2.6k
2
votes
0
replies
2.0k
views
Answer:
Answer: how to understand the P value of the Deseq2 results
3.1 years ago by
Michael Love
★ 2.6k
1
vote
0
replies
2.1k
views
Answer:
A: DESEq2 error - 'DESeqDataSet' object superclass 'RectangularData' not defined in
3.3 years ago by
Michael Love
★ 2.6k
1
vote
0
replies
2.9k
views
Answer:
C: How is the bootstrapping information from kallisto treated in DeSeq2 when import
3.7 years ago by
Michael Love
★ 2.6k
1
vote
1
reply
4.1k
views
Answer:
A: DESeq2 analysis with covariates with and without log transformation
3.9 years ago by
Michael Love
★ 2.6k
7
votes
0
replies
5.7k
views
Answer:
A: How to import RSEM results to DESeq2 for differential analysis
updated 4.2 years ago by
ATpoint
82k • written 6.4 years ago by
Michael Love
★ 2.6k
2
votes
1
reply
10k
views
Answer:
C: Is a simple Wilcoxon rank sum test good enough to identify differentially expres
4.3 years ago by
Michael Love
★ 2.6k
0
votes
1
reply
8.9k
views
Answer:
A: To What Degree Could We Determine Whether A Gene Is Expressed?
updated 4.4 years ago by
Ram
44k • written 10.1 years ago by
Michael Love
★ 2.6k
3
votes
2
replies
4.2k
views
Answer:
Answer: Is inspection and correction of pvalues still needed in DESeq2?
updated 17 months ago by
Ram
44k • written 8.9 years ago by
Michael Love
★ 2.6k
1
vote
2
replies
8.2k
views
Answer:
A: "Duplicate rownames not allowed" when the rownames are not duplicated
5.6 years ago by
Michael Love
★ 2.6k
0
votes
0
replies
2.7k
views
Answer:
A: what's the meaning of a Concordance at the Top plot(CAT plot)
6.6 years ago by
Michael Love
★ 2.6k
7
votes
1
reply
26k
views
Answer:
A: Gene Set Enrichment Analysis after DESeq2
6.6 years ago by
Michael Love
★ 2.6k
3
votes
1
reply
2.9k
views
Answer:
A: Efficient way to run a DESeq2 analysis with many design formulae
6.7 years ago by
Michael Love
★ 2.6k
2
votes
1
reply
5.1k
views
Answer:
A: Why DESeq2 in parallel mode is slower than normal?!
7.0 years ago by
Michael Love
★ 2.6k
2
votes
0
replies
4.0k
views
Answer:
A: How to define a non differentially expressed gene?
7.1 years ago by
Michael Love
★ 2.6k
0
votes
0
replies
4.5k
views
Answer:
A: DESeq2 - how to build design for multiple paired samples before/after with 2 con
7.3 years ago by
Michael Love
★ 2.6k
0
votes
0
replies
3.2k
views
Answer:
A: DESeqDataSetFromMatrix Error in if/while (condition) {: missing Value where TRUE
7.4 years ago by
Michael Love
★ 2.6k
3
votes
1
reply
1.6k
views
Answer:
C: Coping with a label imbalance in DESeq2
7.7 years ago by
Michael Love
★ 2.6k
3
votes
1
reply
45k
views
Answer:
A: Up-to-date RNA-Seq Analysis Training/Courses/Papers (July 2016)
7.8 years ago by
Michael Love
★ 2.6k
1
vote
0
replies
2.6k
views
Answer:
A: The best test for the two conditional problem.
8.0 years ago by
Michael Love
★ 2.6k
0
votes
0
replies
3.3k
views
Answer:
A: clustering from breast cancer RNA-seq data
8.0 years ago by
Michael Love
★ 2.6k
2
votes
0
replies
8.7k
views
Answer:
A: Time course experiments in DESeq2
8.1 years ago by
Michael Love
★ 2.6k
2
votes
1
reply
5.1k
views
Answer:
A: Using 'tximport' library for downstream DGE after quantifying with Kallisto
8.1 years ago by
Michael Love
★ 2.6k
18
votes
1
reply
36k
views
Answer:
A: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
8.2 years ago by
Michael Love
★ 2.6k
2
votes
1
reply
8.3k
views
Answer:
A: following Kallisto with DESeq2 using tximport package
8.3 years ago by
Michael Love
★ 2.6k
1
vote
0
replies
4.7k
views
Answer:
A: Shrinking fold change and dispersion for RNA-seq data ( DESeq2)
8.6 years ago by
Michael Love
★ 2.6k
5
votes
0
replies
4.8k
views
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
vote
1
reply
13k
views
Answer:
A: Deseq2 gene name annotation
8.8 years ago by
Michael Love
★ 2.6k
1
vote
0
replies
2.7k
views
Answer:
A: Running DESeqDataSet with 4 factors?
8.8 years ago by
Michael Love
★ 2.6k
0
votes
0
replies
4.6k
views
Answer:
Answer: Deseq web-based (with GUI)
updated 18 months ago by
Ram
44k • written 8.8 years ago by
Michael Love
★ 2.6k
3
votes
1
reply
9.8k
views
Answer:
Answer: How to remove batch effect from RNA-seq data?
updated 18 months ago by
Ram
44k • written 8.9 years ago by
Michael Love
★ 2.6k
5
votes
0
replies
5.0k
views
Answer:
A: DESeq2: different log2FC results when using subset of data
8.9 years ago by
Michael Love
★ 2.6k
2
votes
0
replies
1.5k
views
Answer:
A: Summarized Experiment _normrange
8.9 years ago by
Michael Love
★ 2.6k
4
votes
0
replies
12k
views
Answer:
Answer: DESeq2 - "all gene-wise dispersion estimates are within 2 orders of magnitude"
updated 17 months ago by
Ram
44k • written 8.9 years ago by
Michael Love
★ 2.6k
4
votes
1
reply
7.6k
views
Answer:
Answer: DESeq2 analysis: huge number of outliers and refitting
updated 17 months ago by
Ram
44k • written 8.9 years ago by
Michael Love
★ 2.6k
6
votes
1
reply
11k
views
Answer:
Answer: fold change vs standardized effect size
updated 15 months ago by
Ram
44k • written 9.0 years ago by
Michael Love
★ 2.6k
1
vote
2
replies
3.1k
views
Answer:
Answer: DESeq2 - Warning message
updated 15 months ago by
Ram
44k • written 9.1 years ago by
Michael Love
★ 2.6k
1
vote
1
reply
3.3k
views
Answer:
A: DESeq2 with 2 factors: problem to fit the negative binomial and weird p-value di
9.1 years ago by
Michael Love
★ 2.6k
2
votes
1
reply
12k
views
Answer:
A: DESeq2 normalisation: is the size of the gene taken into account?
9.1 years ago by
Michael Love
★ 2.6k
1
vote
1
reply
3.9k
views
Answer:
Answer: DESeq2: invalid class “GRangesList” object
updated 2.0 years ago by
Ram
44k • written 9.2 years ago by
Michael Love
★ 2.6k
2
votes
1
reply
4.3k
views
Answer:
Answer: [DESeq2] Little Error in seq_len(nrow(modelMatrix)) while starting DESeq()
updated 2.1 years ago by
Ram
44k • written 9.2 years ago by
Michael Love
★ 2.6k
36
votes
0
replies
22k
views
Answer:
Answer: Can someone please explain in simple terms how DESeq2 works?
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
Michael Love
★ 2.6k
62 results • Page
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