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RNAseq123
•
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12
votes
4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.3 years ago by
Gordon Smyth
50k • written 6.9 years ago by
wd
▴ 30
5
votes
6
replies
2.5k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.1 years ago • updated 2.0 years ago
Alan
• 0
2
votes
1
reply
1.0k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
Mikołaj Mierzejewski
• 0
2
votes
5
replies
1.0k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Istvan Albert
▴ 50
1
vote
1
reply
334
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
kaurprab
• 0
1
vote
3
replies
4.4k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 3.3 years ago by
mmicky5050
• 0
1
vote
1
reply
1.3k
views
featureCounts running too long
RNAseq123
updated 3 months ago by
difraiadomenico
• 0 • written 3.2 years ago by
demirkalecy
▴ 10
1
vote
6
replies
3.2k
views
KEGG enrichment analysis for non model organism
RNAseq123
17 months ago
afsanarupa1
• 0
1
vote
1
reply
711
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 19 months ago by
ATpoint
★ 4.1k • written 20 months ago by
Mohamed
▴ 30
1
vote
1
reply
169
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 10 days ago by
Gordon Smyth
50k • written 14 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
2
replies
542
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
14 months ago
fatemeh.peimani
• 0
0
votes
0
replies
507
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.2 years ago
rpokhre2
• 0
0
votes
1
reply
814
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
kusum
• 0
0
votes
3
replies
827
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 16 months ago by
Michael Love
41k • written 16 months ago by
irish.prg
• 0
0
votes
0
replies
550
views
Plotting a line plot for genes across 4-species
RNAseq123
21 months ago
Mohamed
▴ 30
0
votes
1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Mohamed
▴ 30
16 results • Page
1 of 1
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Replies
Comment: Couldn't connect to server while using "pathways"
by
ATpoint
★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of unavailability.…
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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