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7
votes
28
replies
6.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 4 months ago by 51k • written 9.3 years ago by ★ 7.9k
9
votes
9
replies
5.5k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.4 years ago by ▴ 130 • written 8.2 years ago by ★ 7.9k
1
vote
2
replies
2.1k
views
Comment: C: Limma analysis with multiple variables
4.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.4k
views
Comment: C: Invalid result error in biomaRt::getBM with archive Ensembl versions
4.1 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
1.4k
views
Comment: C: Invalid result error in biomaRt::getBM with archive Ensembl versions
4.1 years ago Ryan C. Thompson ★ 7.9k
1
vote
5
replies
1.4k
views
Invalid result error in biomaRt::getBM with archive Ensembl versions
biomart
updated 4.1 years ago by 66k • written 4.1 years ago by ★ 7.9k
0
votes
1
reply
1.0k
views
Comment: C: Nested Random Effect in LIMMA: Is It Possible?
4.6 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.2k
views
Comment: C: Making sense out of makeContrasts and using coefficents for contrasts
5.4 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
5.5k
views
Answer: A: Random Effect in DESeq2
5.4 years ago Ryan C. Thompson ★ 7.9k
0
votes
2
replies
1.2k
views
Comment: C: Making sense out of makeContrasts and using coefficents for contrasts
5.4 years ago Ryan C. Thompson ★ 7.9k
3
votes
0
replies
2.6k
views
Answer: A: edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
928
views
Comment: C: Appropriate design formula for DESeq2 from principles
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
3.2k
views
Comment: C: Order of contrasts.fit call (before or after eBayes)
5.4 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
3.2k
views
Comment: C: Order of contrasts.fit call (before or after eBayes)
5.4 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
3.2k
views
Answer: A: Order of contrasts.fit call (before or after eBayes)
5.4 years ago Ryan C. Thompson ★ 7.9k
6
votes
0
replies
1.9k
views
Answer: A: LIMMA dupcor() function time issue.
5.4 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
2.9k
views
Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
5.4 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
2.9k
views
Comment: C: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
2.0k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
2
replies
2.0k
views
Answer: A: Taking into account strong batch effect in microarray differential expression an
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
0
replies
2.0k
views
Comment: C: Taking into account strong batch effect in microarray differential expression an
5.4 years ago Ryan C. Thompson ★ 7.9k
1
vote
1
reply
1.9k
views
Answer: A: Filtering, minimum sample number, and condition in edgeR
5.6 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.3k
views
Comment: C: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
5.6 years ago Ryan C. Thompson ★ 7.9k
2
votes
3
replies
1.3k
views
Answer: A: Are spurious correlations possible in correlating two DESeq2 foldchanges compute
5.6 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
43k
views
Answer: A: What is colData? How do I make one?
5.6 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
902
views
Answer: A: [Deseq2] Estimating size factors using samples which have been excluded for QC
5.6 years ago Ryan C. Thompson ★ 7.9k
5
votes
0
replies
4.4k
views
Answer: A: Finding DE genes from RNA-seq data
5.7 years ago Ryan C. Thompson ★ 7.9k
3
votes
2
replies
802
views
Is it ok to use decideTests on linearly dependent contrasts?
limma decidetests
updated 5.7 years ago by 51k • written 5.7 years ago by ★ 7.9k
0
votes
0
replies
3.2k
views
Comment: C: Dispersion fit and p-value distributions
5.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
3.2k
views
Comment: C: Dispersion fit and p-value distributions
5.7 years ago Ryan C. Thompson ★ 7.9k
1
vote
2
replies
3.2k
views
Answer: A: Dispersion fit and p-value distributions
5.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
3.2k
views
Comment: C: Dispersion fit and p-value distributions
5.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
899
views
Comment: C: DEseq2 - minimum number of genes
5.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
742
views
Comment: C: DESeq2 normalization Factor Matrix to correct for uneven targeted sequencing cov
5.7 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
4.9k
views
Comment: C: Batch correction when only some subjects have replicates across batches
5.8 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
4.9k
views
Comment: C: Batch correction when only some subjects have replicates across batches
5.8 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
4.9k
views
Comment: C: Batch correction when only some subjects have replicates across batches
5.8 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
7.0k
views
Comment: C: Voom transformation from counts and normalization to negative values
5.8 years ago Ryan C. Thompson ★ 7.9k
1
vote
1
reply
7.0k
views
Comment: C: Voom transformation from counts and normalization to negative values
5.8 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
7.0k
views
Comment: C: Voom transformation from counts and normalization to negative values
5.8 years ago Ryan C. Thompson ★ 7.9k
5
votes
1
reply
7.0k
views
Answer: A: Voom transformation from counts and normalization to negative values
5.8 years ago Ryan C. Thompson ★ 7.9k
1
vote
2
replies
2.2k
views
Answer: A: Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
5.8 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
1.2k
views
Comment: C: How do I discern if a magnitude difference in expression is up-regulation in one
5.8 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.1k
views
Comment: C: Limma: Differential expression for micro RNA sequence data
5.8 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.8k
views
Comment: C: skewed differentially expressed gene results - DESeq2
5.9 years ago Ryan C. Thompson ★ 7.9k
0
votes
2
replies
1.8k
views
Answer: A: skewed differentially expressed gene results - DESeq2
5.9 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.8k
views
Comment: C: skewed differentially expressed gene results - DESeq2
5.9 years ago Ryan C. Thompson ★ 7.9k
0
votes
0
replies
1.5k
views
Comment: C: unexpected p-value histogram in edgeR
6.0 years ago Ryan C. Thompson ★ 7.9k
0
votes
1
reply
1.5k
views
Comment: C: unexpected p-value histogram in edgeR
6.0 years ago Ryan C. Thompson ★ 7.9k
2
votes
1
reply
1.3k
views
Answer: A: DESseq2: Why can the dispersion be generelized over the conditions?
6.0 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 1 of 17
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