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rnaseq123
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308
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
6 months ago
tim.meese
• 0
1
vote
2
replies
516
views
Improving the design matrices vignette in RNAseq123
RNAseq123
11 months ago • updated 10 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
755
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 16 months ago by
ATpoint
★ 4.8k • written 16 months ago by
kaurprab
• 0
0
votes
2
replies
933
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
2.1 years ago
fatemeh.peimani
• 0
0
votes
3
replies
1.3k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
irish.prg
• 0
1
vote
6
replies
5.4k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.3 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 2.3 years ago by
Gordon Smyth
52k • written 2.3 years ago by
Istvan Albert
▴ 50
0
votes
1
reply
2.3k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Mohamed
▴ 30
1
vote
1
reply
1.0k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.5 years ago by
ATpoint
★ 4.8k • written 2.5 years ago by
Mohamed
▴ 30
0
votes
0
replies
781
views
Plotting a line plot for genes across 4-species
RNAseq123
2.7 years ago
Mohamed
▴ 30
2
votes
1
reply
1.4k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.8 years ago by
Gordon Smyth
52k • written 2.8 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.7k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.9 years ago
Alan
• 0
0
votes
1
reply
1.1k
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
kusum
• 0
1
vote
1
reply
2.0k
views
featureCounts running too long
RNAseq123
updated 13 months ago by
difraiadomenico
• 0 • written 4.0 years ago by
demirkalecy
▴ 10
0
votes
0
replies
731
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
4.1 years ago
rpokhre2
• 0
1
vote
3
replies
5.8k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 4.2 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 6.2 years ago by
Gordon Smyth
52k • written 7.8 years ago by
wd
▴ 30
17 results • Page
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Comment: Package developing and interoperation with Bioconductor
by
shepherl
4.1k
Using an example with SummarizedExperiment would satisfy the requirement; however the package should take the object directly and not just…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
by
Sofia
• 0
1. I have tried to update the packages and R but to no avail. I keep getting either this error or : `Error in H5Fclose(file$H5Identifier) …
Comment: Validity of SingleR with very small bulk RNAseq reference
by
Rohit
• 0
Hi @nhaus So, what did you end up doing in such a scenario? I am facing a similar challenge
Comment: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
Joshua Llano
• 0
Thank you for your reply James. I was worried that it was my mistake.
Comment: Annotation package for Manduca sexta
by
GA
▴ 10
Thank you!
Votes
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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