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RNASeq123
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205
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
7 weeks ago • updated 6 weeks ago
tim.meese
• 0
1
vote
2
replies
438
views
Improving the design matrices vignette in RNAseq123
RNAseq123
6 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
607
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
kaurprab
• 0
0
votes
2
replies
798
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
21 months ago
fatemeh.peimani
• 0
0
votes
3
replies
1.2k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 23 months ago by
Michael Love
42k • written 23 months ago by
irish.prg
• 0
1
vote
6
replies
4.4k
views
KEGG enrichment analysis for non model organism
RNAseq123
23 months 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 23 months ago by
Gordon Smyth
51k • written 24 months ago by
Istvan Albert
▴ 50
0
votes
1
reply
1.9k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.0 years ago by
James W. MacDonald
67k • written 2.0 years ago by
Mohamed
▴ 30
1
vote
1
reply
917
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.2 years ago by
ATpoint
★ 4.5k • written 2.2 years ago by
Mohamed
▴ 30
0
votes
0
replies
702
views
Plotting a line plot for genes across 4-species
RNAseq123
2.3 years ago
Mohamed
▴ 30
2
votes
1
reply
1.2k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.4 years ago by
Gordon Smyth
51k • written 2.4 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.6 years ago
Alan
• 0
0
votes
1
reply
966
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
kusum
• 0
1
vote
1
reply
1.8k
views
featureCounts running too long
RNAseq123
updated 9 months ago by
difraiadomenico
• 0 • written 3.7 years ago by
demirkalecy
▴ 10
0
votes
0
replies
657
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.8 years ago
rpokhre2
• 0
1
vote
3
replies
5.2k
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
51k • written 7.4 years ago by
wd
▴ 30
17 results • Page
1 of 1
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Replies
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge
by
Robert Castelo
★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results
by
ATpoint
★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ]
by
Gordon Smyth
51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge
by
rania.alanany
• 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model
by
abadgerw
• 0
@gabrielhoffman any insight?
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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Robert Castelo
★ 3.4k
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to
Michael Stadler
▴ 350
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ATpoint
★ 4.5k
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James W. MacDonald
67k
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Stefano Mangiola
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