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RNAseq123
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242
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
3 months ago
tim.meese
• 0
1
vote
2
replies
462
views
Improving the design matrices vignette in RNAseq123
RNAseq123
8 months ago • updated 7 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
651
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 13 months ago by
ATpoint
★ 4.6k • written 13 months ago by
kaurprab
• 0
0
votes
2
replies
841
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 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
irish.prg
• 0
1
vote
6
replies
4.6k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.1 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 2.1 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 2.2 years ago by
Mohamed
▴ 30
1
vote
1
reply
939
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
730
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
3.4k
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
997
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
1.9k
views
featureCounts running too long
RNAseq123
updated 11 months ago by
difraiadomenico
• 0 • written 3.8 years ago by
demirkalecy
▴ 10
0
votes
0
replies
671
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 4.0 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 6.0 years ago by
Gordon Smyth
52k • written 7.6 years ago by
wd
▴ 30
17 results • Page
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character
by
ATpoint
★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format
by
ControlF5
• 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open!
by
Alan Downey
• 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
by
O'Brien
• 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts
by
O'Brien
• 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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