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RNAseq123
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261
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
4 months ago
tim.meese
• 0
1
vote
2
replies
477
views
Improving the design matrices vignette in RNAseq123
RNAseq123
9 months ago • updated 8 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
677
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 14 months ago by
ATpoint
★ 4.6k • written 14 months ago by
kaurprab
• 0
0
votes
2
replies
866
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
23 months ago
fatemeh.peimani
• 0
0
votes
3
replies
1.3k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
irish.prg
• 0
1
vote
6
replies
4.8k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.1 years ago
afsanarupa1
• 0
2
votes
5
replies
1.4k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 2.2 years ago by
Gordon Smyth
52k • written 2.2 years ago by
Istvan Albert
▴ 50
0
votes
1
reply
2.1k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.2 years ago by
James W. MacDonald
67k • written 2.2 years ago by
Mohamed
▴ 30
1
vote
1
reply
967
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.4 years ago by
ATpoint
★ 4.6k • written 2.4 years ago by
Mohamed
▴ 30
0
votes
0
replies
744
views
Plotting a line plot for genes across 4-species
RNAseq123
2.5 years ago
Mohamed
▴ 30
2
votes
1
reply
1.3k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.6 years ago by
Gordon Smyth
52k • written 2.6 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.5k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.8 years ago
Alan
• 0
0
votes
1
reply
1.0k
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
kusum
• 0
1
vote
1
reply
1.9k
views
featureCounts running too long
RNAseq123
updated 12 months ago by
difraiadomenico
• 0 • written 3.9 years ago by
demirkalecy
▴ 10
0
votes
0
replies
685
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
4.0 years ago
rpokhre2
• 0
1
vote
3
replies
5.5k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 4.1 years ago by
mmicky5050
• 0
12
votes
4
replies
4.9k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 6.1 years ago by
Gordon Smyth
52k • written 7.6 years ago by
wd
▴ 30
17 results • Page
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Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Prakash Sah
• 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
ATpoint
★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
Votes
A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
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