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Comment: Comment: How to run getSeq() on a GRanges object with invalid DNA letters?
2.9 years ago Jon Bråte ▴ 250
4
votes
9
replies
1.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 250
1
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0
replies
1.7k
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Comment: Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
3.2 years ago Jon Bråte ▴ 250
1
vote
1
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1.7k
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Comment: Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
3.2 years ago Jon Bråte ▴ 250
0
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0
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657
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Comment: C: Using confect score from the topconfects package to filter DE-genes
4.0 years ago Jon Bråte ▴ 250
1
vote
2
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657
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Using confect score from the topconfects package to filter DE-genes
topconfects
updated 4.0 years ago by ▴ 100 • written 4.0 years ago by ▴ 250
0
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0
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2.1k
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Comment: C: Upper-quartile normalization before RUVg normalization?
5.0 years ago Jon Bråte ▴ 250
0
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1
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2.1k
views
Comment: C: Upper-quartile normalization before RUVg normalization?
5.0 years ago Jon Bråte ▴ 250
2
votes
4
replies
2.1k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.0 years ago by ▴ 950 • written 5.0 years ago by ▴ 250
0
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0
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1.3k
views
Comment: C: How to remove samples from EDAseq SeqExpressionSeq
5.3 years ago Jon Bråte ▴ 250
1
vote
2
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1.3k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.3 years ago by ▴ 950 • written 5.3 years ago by ▴ 250
0
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0
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755
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Comment: C: DESeq2: How to get sizeFactor per library when importing counts with tximport?
6.1 years ago Jon Bråte ▴ 250
2
votes
2
replies
755
views
DESeq2: How to get sizeFactor per library when importing counts with tximport?
deseq2
updated 6.1 years ago by 41k • written 6.1 years ago by ▴ 250
0
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0
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6.3k
views
Comment: C: DESeq2: Question about the alpha in summary() and results()
6.3 years ago Jon Bråte ▴ 250
3
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14
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6.3k
views
DESeq2: Question about the alpha in summary() and results()
deseq2
updated 15 months ago by ▴ 10 • written 6.3 years ago by ▴ 250
0
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0
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4.2k
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Comment: C: rtracklayer: how to export gff file with gene names included?
7.1 years ago Jon Bråte ▴ 250
3
votes
2
replies
4.2k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 250
0
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0
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4.5k
views
Answer: A: miRNA-seq data analysis
7.1 years ago Jon Bråte ▴ 250
0
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1
reply
2.8k
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Comment: C: Why does rlog and vst use normalized counts?
7.3 years ago Jon Bråte ▴ 250
3
votes
5
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2.8k
views
Why does rlog and vst use normalized counts?
deseq2
updated 7.3 years ago by ★ 13k • written 7.3 years ago by ▴ 250
7
votes
13
replies
2.2k
views
Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
7.5 years ago • updated 7.4 years ago Jon Bråte ▴ 250
0
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0
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2.2k
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Answer: A: Test whether expression levels of two gene sets are significantly different
7.4 years ago Jon Bråte ▴ 250
0
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1
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2.2k
views
Comment: C: Test whether expression levels of two gene sets are significantly different
7.5 years ago Jon Bråte ▴ 250
3
votes
3
replies
16k
views
Error in Knit R Markdown document (could not find function "Biocexptpkg")
rmarkdown rstudio knitr
7.5 years ago Jon Bråte ▴ 250
0
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0
replies
16k
views
Answer: A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
7.5 years ago Jon Bråte ▴ 250
32
votes
10
replies
38k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 12 months ago by • 0 • written 10.4 years ago by ▴ 250
0
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0
replies
19k
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Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
7.9 years ago Jon Bråte ▴ 250
0
votes
1
reply
19k
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Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
7.9 years ago Jon Bråte ▴ 250
0
votes
1
reply
2.1k
views
Comment: C: Using DESeq2 on CEL-Seq data
8.1 years ago Jon Bråte ▴ 250
0
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1
reply
3.3k
views
Answer: A: HTSeq-count on several gff3/gtf files for use in DESeq2
8.2 years ago Jon Bråte ▴ 250
1
vote
3
replies
3.3k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff
8.2 years ago Jon Bråte ▴ 250
3
votes
4
replies
2.0k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
8.3 years ago Jon Bråte ▴ 250
0
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1
reply
2.0k
views
Answer: A: Large differences in sample clustering using cummeRbund (csDendro) and rlog-dist
8.3 years ago Jon Bråte ▴ 250
0
votes
0
replies
4.9k
views
Comment: C: Using goseq on non-model organism - how to define genome?
8.3 years ago Jon Bråte ▴ 250
1
vote
1
reply
4.9k
views
Comment: C: Using goseq on non-model organism - how to define genome?
8.4 years ago Jon Bråte ▴ 250
1
vote
1
reply
4.9k
views
Comment: C: Using goseq on non-model organism - how to define genome?
8.4 years ago Jon Bråte ▴ 250
5
votes
7
replies
4.9k
views
Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 250
0
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0
replies
4.6k
views
Comment: C: Questions about GOseq after DESeq2
8.4 years ago Jon Bråte ▴ 250
0
votes
1
reply
1.4k
views
Error in export.gff from rtracklayer
rtracklayer gff
8.6 years ago Jon Bråte ▴ 250
0
votes
1
reply
1.1k
views
Is it possible (or does it make sense) to display two different gene sets in one PCA-plot?
pca deseq2 rnaseq
updated 8.6 years ago by 41k • written 8.6 years ago by ▴ 250
3
votes
5
replies
2.8k
views
(how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
deseq2 cummerbund cufflinks
updated 8.7 years ago by 41k • written 8.7 years ago by ▴ 250
0
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0
replies
1.7k
views
Comment: C: Error message running DE-test in Monocle
8.8 years ago Jon Bråte ▴ 250
1
vote
2
replies
1.7k
views
Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 8.8 years ago by • 0 • written 9.0 years ago by ▴ 250
0
votes
1
reply
5.2k
views
Comment: C: Can I use the WGCNA dendrogram to display a heatmap of gene expression?
9.0 years ago Jon Bråte ▴ 250
0
votes
1
reply
5.2k
views
Comment: C: Can I use the WGCNA dendrogram to display a heatmap of gene expression?
9.0 years ago Jon Bråte ▴ 250
2
votes
5
replies
5.2k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 9.0 years ago by ★ 1.5k • written 9.0 years ago by ▴ 250
2
votes
3
replies
1.4k
views
Need advice on normalization of SMART-amplified RNA-Seq data
normalization rna-seq deseq2 edger smart
updated 9.1 years ago by ★ 7.9k • written 9.1 years ago by ▴ 250
0
votes
0
replies
1.4k
views
Comment: C: Need advice on normalization of SMART-amplified RNA-Seq data
9.1 years ago Jon Bråte ▴ 250
0
votes
0
replies
5.9k
views
Comment: C: Adjust p-values of a matrix of p-values
9.4 years ago Jon Bråte ▴ 250
4
votes
2
replies
5.9k
views
Adjust p-values of a matrix of p-values
multtest
updated 9.4 years ago by 50k • written 9.4 years ago by ▴ 250
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