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rnaseq123
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
11 weeks ago
tim.meese
• 0
1
vote
2
replies
456
views
Improving the design matrices vignette in RNAseq123
RNAseq123
8 months ago • updated 7 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
643
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 12 months ago by
ATpoint
★ 4.6k • written 12 months ago by
kaurprab
• 0
0
votes
2
replies
829
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
22 months ago
fatemeh.peimani
• 0
0
votes
3
replies
1.2k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 24 months ago by
Michael Love
43k • written 24 months ago by
irish.prg
• 0
1
vote
6
replies
4.6k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.0 years ago
afsanarupa1
• 0
2
votes
5
replies
1.3k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 2.0 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Istvan Albert
▴ 50
0
votes
1
reply
2.0k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.1 years ago by
James W. MacDonald
67k • written 2.1 years ago by
Mohamed
▴ 30
1
vote
1
reply
935
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.3 years ago by
ATpoint
★ 4.6k • written 2.3 years ago by
Mohamed
▴ 30
0
votes
0
replies
724
views
Plotting a line plot for genes across 4-species
RNAseq123
2.4 years ago
Mohamed
▴ 30
2
votes
1
reply
1.3k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.5 years ago by
Gordon Smyth
52k • written 2.5 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.3k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.7 years ago
Alan
• 0
0
votes
1
reply
991
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.4 years ago by
Kevin Blighe
★ 4.0k • written 3.4 years ago by
kusum
• 0
1
vote
1
reply
1.8k
views
featureCounts running too long
RNAseq123
updated 10 months ago by
difraiadomenico
• 0 • written 3.8 years ago by
demirkalecy
▴ 10
0
votes
0
replies
666
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.9 years ago
rpokhre2
• 0
1
vote
3
replies
5.4k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 3.9 years ago by
mmicky5050
• 0
12
votes
4
replies
4.8k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.9 years ago by
Gordon Smyth
52k • written 7.5 years ago by
wd
▴ 30
17 results • Page
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Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
Just fit a model `~condition + experiment` where `condition` has three levels A, B and C. Ideally, use limma and include duplicate correlat…
Comment: Error in get_anno_data(ontology) : ontology not supported yet...
by
GODseeker
• 0
thank u so much ,god bless u,my dear friend.
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet...
by
Guido Hooiveld
★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Votes
A: Advice on correcting for batch effect using DESeq2
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
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