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RNAseq123
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349
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
7 months ago
tim.meese
• 0
1
vote
2
replies
540
views
Improving the design matrices vignette in RNAseq123
RNAseq123
12 months ago • updated 11 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
785
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 17 months ago by
ATpoint
★ 4.8k • written 17 months ago by
kaurprab
• 0
0
votes
2
replies
971
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
2.2 years ago
fatemeh.peimani
• 0
0
votes
3
replies
1.4k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
irish.prg
• 0
1
vote
6
replies
5.6k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.4 years ago
afsanarupa1
• 0
2
votes
5
replies
1.5k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 2.4 years ago by
Gordon Smyth
52k • written 2.4 years ago by
Istvan Albert
▴ 50
0
votes
1
reply
2.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Mohamed
▴ 30
1
vote
1
reply
1.1k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.6 years ago by
ATpoint
★ 4.8k • written 2.6 years ago by
Mohamed
▴ 30
0
votes
0
replies
803
views
Plotting a line plot for genes across 4-species
RNAseq123
2.8 years ago
Mohamed
▴ 30
2
votes
1
reply
1.5k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.9 years ago by
Gordon Smyth
52k • written 2.9 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.9k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
3.0 years ago
Alan
• 0
0
votes
1
reply
1.1k
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
kusum
• 0
1
vote
1
reply
2.1k
views
featureCounts running too long
RNAseq123
updated 15 months ago by
difraiadomenico
• 0 • written 4.1 years ago by
demirkalecy
▴ 10
0
votes
0
replies
749
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
4.2 years ago
rpokhre2
• 0
1
vote
3
replies
6.0k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 4.3 years ago by
mmicky5050
• 0
12
votes
4
replies
5.0k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 6.3 years ago by
Gordon Smyth
52k • written 7.9 years ago by
wd
▴ 30
17 results • Page
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Comment: Discrepancies in normalised count data vs unnormalised
by
AMgroup
• 0
Thank you for your reply Here are the count plots for one example CD44: normalised: ![enter image description here][1] unnormalised: !…
Comment: Discrepancies in normalised count data vs unnormalised
by
ATpoint
★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Comment: Cannot extract size factor from DESeq2 analysis
by
s.malik
• 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function
by
Vishnu
• 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2
by
Tom
• 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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