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7
votes
28
replies
8.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 21 months ago by 53k • written 10.6 years ago by ★ 7.9k
9
votes
9
replies
6.5k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.7 years ago by ▴ 150 • written 9.6 years ago by ★ 7.9k
1
vote
2
replies
3.0k
views
Comment: C: Limma analysis with multiple variables
5.4 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.9k
views
Comment: C: Invalid result error in biomaRt::getBM with archive Ensembl versions
5.4 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
1.9k
views
Comment: C: Invalid result error in biomaRt::getBM with archive Ensembl versions
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
5
replies
1.9k
views
Invalid result error in biomaRt::getBM with archive Ensembl versions
biomart
updated 5.4 years ago by 68k • written 5.4 years ago by ★ 7.9k
0
votes
1
reply
1.5k
views
Comment: C: Nested Random Effect in LIMMA: Is It Possible?
5.9 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.6k
views
Comment: C: Making sense out of makeContrasts and using coefficents for contrasts
6.7 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
7.5k
views
Answer: A: Random Effect in DESeq2
6.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
2
replies
1.6k
views
Comment: C: Making sense out of makeContrasts and using coefficents for contrasts
6.7 years ago Ryan C. Thompson ★ 7.9k
3
votes
0
replies
3.3k
views
Answer: A: edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
6.7 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
1.6k
views
Comment: C: Appropriate design formula for DESeq2 from principles
6.7 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
4.5k
views
Comment: C: Order of contrasts.fit call (before or after eBayes)
6.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
4.5k
views
Comment: C: Order of contrasts.fit call (before or after eBayes)
6.7 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
4.5k
views
Answer: A: Order of contrasts.fit call (before or after eBayes)
6.7 years ago Ryan C. Thompson ★ 7.9k
6
votes
0
replies
2.6k
views
Answer: A: LIMMA dupcor() function time issue.
6.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
3.8k
views
Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
6.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
3.8k
views
Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
6.7 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
2.7k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
6.8 years ago Ryan C. Thompson ★ 7.9k
1
vote
2
replies
2.7k
views
Answer: A: Taking into account strong batch effect in microarray differential expression an
6.8 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
2.7k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
6.8 years ago Ryan C. Thompson ★ 7.9k
1
vote
1
reply
2.9k
views
Answer: A: Filtering, minimum sample number, and condition in edgeR
6.9 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.9k
views
Comment: C: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
7.0 years ago Ryan C. Thompson ★ 7.9k
2
votes
3
replies
1.9k
views
Answer: A: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
7.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
50k
views
Answer: A: What is colData? How do I make one?
7.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.2k
views
Answer: A: [Deseq2] Estimating size factors using samples which have been excluded for QC
7.0 years ago Ryan C. Thompson ★ 7.9k
5
votes
0
replies
6.5k
views
Answer: A: Finding DE genes from RNA-seq data
7.0 years ago Ryan C. Thompson ★ 7.9k
3
votes
2
replies
1.1k
views
Is it ok to use decideTests on linearly dependent contrasts?
limma decidetests
updated 7.0 years ago by 53k • written 7.0 years ago by ★ 7.9k
0
votes
0
replies
4.4k
views
Comment: C: Dispersion fit and p-value distributions
7.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
4.4k
views
Comment: C: Dispersion fit and p-value distributions
7.0 years ago Ryan C. Thompson ★ 7.9k
1
vote
2
replies
4.4k
views
Answer: A: Dispersion fit and p-value distributions
7.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
4.4k
views
Comment: C: Dispersion fit and p-value distributions
7.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
1.2k
views
Comment: C: DEseq2 - minimum number of genes
7.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.0k
views
Comment: C: DESeq2 normalization Factor Matrix to correct for uneven targeted sequencing cov
7.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
7.2k
views
Comment: C: Batch correction when only some subjects have replicates across batches
7.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
7.2k
views
Comment: C: Batch correction when only some subjects have replicates across batches
7.1 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
7.2k
views
Comment: C: Batch correction when only some subjects have replicates across batches
7.1 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
8.8k
views
Comment: C: Voom transformation from counts and normalization to negative values
7.1 years ago Ryan C. Thompson ★ 7.9k
1
vote
1
reply
8.8k
views
Comment: C: Voom transformation from counts and normalization to negative values
7.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
8.8k
views
Comment: C: Voom transformation from counts and normalization to negative values
7.1 years ago Ryan C. Thompson ★ 7.9k
5
votes
1
reply
8.8k
views
Answer: A: Voom transformation from counts and normalization to negative values
7.1 years ago Ryan C. Thompson ★ 7.9k
1
vote
2
replies
3.0k
views
Answer: A: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
7.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
1.8k
views
Comment: C: How do I discern if a magnitude difference in expression is up-regulation in one
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.5k
views
Comment: C: Limma: Differential expression for micro RNA sequence data
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
2.5k
views
Comment: C: skewed differentially expressed gene results - DESeq2
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
2
replies
2.5k
views
Answer: A: skewed differentially expressed gene results - DESeq2
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
2.5k
views
Comment: C: skewed differentially expressed gene results - DESeq2
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
2.1k
views
Comment: C: unexpected p-value histogram in edgeR
7.3 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
2.1k
views
Comment: C: unexpected p-value histogram in edgeR
7.3 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
1.8k
views
Answer: A: DESseq2: Why can the dispersion be generelized over the conditions?
7.4 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 1 of 17
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