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6.1k
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Comment: Comment: Installing Bioconductor packages in Docker
4 months ago Jon Bråte ▴ 260
0
votes
1
reply
2.0k
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Comment: Comment: How to run getSeq() on a GRanges object with invalid DNA letters?
3.4 years ago Jon Bråte ▴ 260
4
votes
9
replies
2.0k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 260
1
vote
0
replies
1.9k
views
Comment: Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
3.7 years ago Jon Bråte ▴ 260
1
vote
1
reply
1.9k
views
Comment: Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
3.7 years ago Jon Bråte ▴ 260
0
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0
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831
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Comment: C: Using confect score from the topconfects package to filter DE-genes
4.5 years ago Jon Bråte ▴ 260
1
vote
2
replies
831
views
Using confect score from the topconfects package to filter DE-genes
topconfects
updated 4.5 years ago by ▴ 100 • written 4.5 years ago by ▴ 260
0
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0
replies
2.6k
views
Comment: C: Upper-quartile normalization before RUVg normalization?
5.5 years ago Jon Bråte ▴ 260
0
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1
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2.6k
views
Comment: C: Upper-quartile normalization before RUVg normalization?
5.5 years ago Jon Bråte ▴ 260
2
votes
4
replies
2.6k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.5 years ago by ▴ 980 • written 5.5 years ago by ▴ 260
0
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0
replies
1.5k
views
Comment: C: How to remove samples from EDAseq SeqExpressionSeq
5.8 years ago Jon Bråte ▴ 260
1
vote
2
replies
1.5k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 5.8 years ago by ▴ 980 • written 5.8 years ago by ▴ 260
0
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0
replies
875
views
Comment: C: DESeq2: How to get sizeFactor per library when importing counts with tximport?
6.6 years ago Jon Bråte ▴ 260
2
votes
2
replies
875
views
DESeq2: How to get sizeFactor per library when importing counts with tximport?
deseq2
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 260
0
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0
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7.2k
views
Comment: C: DESeq2: Question about the alpha in summary() and results()
6.8 years ago Jon Bråte ▴ 260
3
votes
14
replies
7.2k
views
DESeq2: Question about the alpha in summary() and results()
deseq2
updated 21 months ago by ▴ 10 • written 6.8 years ago by ▴ 260
0
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0
replies
4.7k
views
Comment: C: rtracklayer: how to export gff file with gene names included?
7.6 years ago Jon Bråte ▴ 260
3
votes
2
replies
4.7k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 260
0
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0
replies
4.9k
views
Answer: A: miRNA-seq data analysis
7.6 years ago Jon Bråte ▴ 260
0
votes
1
reply
3.3k
views
Comment: C: Why does rlog and vst use normalized counts?
7.9 years ago Jon Bråte ▴ 260
3
votes
5
replies
3.3k
views
Why does rlog and vst use normalized counts?
deseq2
updated 7.9 years ago by ★ 13k • written 7.9 years ago by ▴ 260
0
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0
replies
2.6k
views
Answer: A: Test whether expression levels of two gene sets are significantly different
8.0 years ago Jon Bråte ▴ 260
7
votes
13
replies
2.6k
views
Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
8.0 years ago Jon Bråte ▴ 260
0
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1
reply
2.6k
views
Comment: C: Test whether expression levels of two gene sets are significantly different
8.0 years ago Jon Bråte ▴ 260
3
votes
3
replies
16k
views
Error in Knit R Markdown document (could not find function "Biocexptpkg")
rmarkdown rstudio knitr
8.1 years ago Jon Bråte ▴ 260
0
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0
replies
16k
views
Answer: A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
8.1 years ago Jon Bråte ▴ 260
34
votes
11
replies
41k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.0 years ago by ▴ 260
0
votes
0
replies
20k
views
Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
8.4 years ago Jon Bråte ▴ 260
0
votes
1
reply
20k
views
Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
8.4 years ago Jon Bråte ▴ 260
0
votes
1
reply
2.3k
views
Comment: C: Using DESeq2 on CEL-Seq data
8.6 years ago Jon Bråte ▴ 260
1
vote
3
replies
3.6k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools deseq2 counts cuffdiff
8.7 years ago Jon Bråte ▴ 260
0
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1
reply
3.6k
views
Answer: A: HTSeq-count on several gff3/gtf files for use in DESeq2
8.7 years ago Jon Bråte ▴ 260
3
votes
4
replies
2.2k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
8.8 years ago Jon Bråte ▴ 260
0
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1
reply
2.2k
views
Answer: A: Large differences in sample clustering using cummeRbund (csDendro) and rlog-dist
8.8 years ago Jon Bråte ▴ 260
0
votes
0
replies
5.3k
views
Comment: C: Using goseq on non-model organism - how to define genome?
8.8 years ago Jon Bråte ▴ 260
1
vote
1
reply
5.3k
views
Comment: C: Using goseq on non-model organism - how to define genome?
8.9 years ago Jon Bråte ▴ 260
1
vote
1
reply
5.3k
views
Comment: C: Using goseq on non-model organism - how to define genome?
8.9 years ago Jon Bråte ▴ 260
5
votes
7
replies
5.3k
views
Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 8.9 years ago by 51k • written 8.9 years ago by ▴ 260
0
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0
replies
4.8k
views
Comment: C: Questions about GOseq after DESeq2
8.9 years ago Jon Bråte ▴ 260
0
votes
1
reply
1.5k
views
Error in export.gff from rtracklayer
rtracklayer gff
9.1 years ago Jon Bråte ▴ 260
0
votes
1
reply
1.2k
views
Is it possible (or does it make sense) to display two different gene sets in one PCA-plot?
pca deseq2 rnaseq
updated 9.2 years ago by 42k • written 9.2 years ago by ▴ 260
3
votes
5
replies
3.0k
views
(how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
deseq2 cummerbund cufflinks
updated 9.2 years ago by 42k • written 9.2 years ago by ▴ 260
0
votes
0
replies
1.9k
views
Comment: C: Error message running DE-test in Monocle
9.3 years ago Jon Bråte ▴ 260
1
vote
2
replies
1.9k
views
Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 9.3 years ago by • 0 • written 9.6 years ago by ▴ 260
0
votes
1
reply
5.6k
views
Comment: C: Can I use the WGCNA dendrogram to display a heatmap of gene expression?
9.5 years ago Jon Bråte ▴ 260
0
votes
1
reply
5.6k
views
Comment: C: Can I use the WGCNA dendrogram to display a heatmap of gene expression?
9.5 years ago Jon Bråte ▴ 260
2
votes
5
replies
5.6k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 9.5 years ago by ★ 1.5k • written 9.5 years ago by ▴ 260
2
votes
3
replies
1.7k
views
Need advice on normalization of SMART-amplified RNA-Seq data
normalization rna-seq deseq2 edger smart
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 260
0
votes
0
replies
1.7k
views
Comment: C: Need advice on normalization of SMART-amplified RNA-Seq data
9.7 years ago Jon Bråte ▴ 260
0
votes
0
replies
6.1k
views
Comment: C: Adjust p-values of a matrix of p-values
10.0 years ago Jon Bråte ▴ 260
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