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RnaSeq
•
reset
0
votes
0
replies
772
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
19 months ago
JG13
• 0
0
votes
1
reply
772
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
cbio
• 0
1
vote
9
replies
3.7k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
adrip
▴ 10
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Ben
▴ 50
2
votes
2
replies
1.1k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 19 months ago by
jessica.anderson
▴ 10 • written 20 months ago by
ttt
• 0
0
votes
6
replies
2.3k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
20 months ago • updated 19 months ago
atan
• 0
3
votes
2
replies
1.3k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
20 months ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
681
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
20 months ago
Bibi
• 0
10
votes
11
replies
3.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 20 months ago by
Sara
• 0 • written 8.4 years ago by
Sylvain Foisy
▴ 80
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
Ashley
• 0
0
votes
3
replies
1.6k
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
james.zhang20
• 0
0
votes
1
reply
900
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 21 months ago by
Michael Love
43k • written 21 months ago by
kcarey
• 0
0
votes
2
replies
839
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 21 months ago by
taur.vil
• 0
0
votes
2
replies
1.3k
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
21 months ago
catv
• 0
5
votes
3
replies
1.7k
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 20 months ago by
Gordon Smyth
53k • written 21 months ago by
Shaimaa Gamal
• 0
0
votes
1
reply
1.5k
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 21 months ago by
Michael Love
43k • written 21 months ago by
09191919
• 0
0
votes
1
reply
1.0k
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Merav
• 0
0
votes
2
replies
2.2k
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
22 months ago
kcarey
• 0
2
votes
2
replies
907
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
22 months ago
Sabiha
▴ 20
0
votes
2
replies
3.6k
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
22 months ago
kcarey
• 0
1
vote
4
replies
960
views
DESeq2 Replicates
DESeq2
RNASeq
22 months ago
kcarey
• 0
1
vote
3
replies
1.2k
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 22 months ago by
swbarnes2
★ 1.4k • written 22 months ago by
sap275
▴ 10
0
votes
4
replies
1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
23 months ago • updated 22 months ago
mperalc
• 0
0
votes
2
replies
1.2k
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
ryann
• 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 22 months ago by
Michael Love
43k • written 23 months ago by
sap275
▴ 10
2
votes
1
reply
791
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 23 months ago by
Michael Love
43k • written 23 months ago by
sap275
▴ 10
3
votes
7
replies
2.0k
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
23 months ago • updated 4 months ago
boczniak767
▴ 740
0
votes
0
replies
799
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
23 months ago
Abril
• 0
2
votes
2
replies
1.8k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
23 months ago
jackafiore
• 0
1
vote
2
replies
2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 2.7 years ago by
informatician
• 0
0
votes
4
replies
1.1k
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
23 months ago
candacenewcome
• 0
1
vote
3
replies
1.3k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
24 months ago • updated 23 months ago
island
• 0
1
vote
3
replies
1.4k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 24 months ago by
georgii.vdovin
• 0
0
votes
1
reply
697
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 24 months ago by
Ram
▴ 220 • written 24 months ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
2.6k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
24 months ago
Sabiha
▴ 20
4
votes
6
replies
1.8k
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 23 months ago by
Gordon Smyth
53k • written 2.0 years ago by
Shaimaa Gamal
• 0
3
votes
1
reply
946
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 2.0 years ago by
Gordon Smyth
53k • written 2.0 years ago by
Shaimaa Gamal
• 0
0
votes
3
replies
1.6k
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 2.0 years ago by
Fayrouz
• 0
0
votes
1
reply
865
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
2.0 years ago
WS
• 0
2
votes
3
replies
3.9k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
Bo
• 0
1
vote
2
replies
1.3k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
2.1 years ago
Sabiha
▴ 20
1
vote
2
replies
1.3k
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
2.1 years ago
drewhaydensteele
• 0
12
votes
5
replies
5.3k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 7 months ago by
Geoff
• 0 • written 2.1 years ago by
annikagable
• 0
0
votes
3
replies
1.4k
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
2.2 years ago • updated 2.1 years ago
Karthik
• 0
1
vote
1
reply
810
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.2 years ago by
pl23
• 0
2
votes
3
replies
1.6k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
2.2 years ago • updated 2.1 years ago
Karthik
• 0
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
2.2 years ago
Manthos
• 0
2
votes
4
replies
1.5k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
2.2 years ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
868
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
Sean
• 0
0
votes
2
replies
1.4k
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 2.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 2.2 years ago by
tangming2005
▴ 200
1,412 results • Page
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Comment: Pairwise comparison of multiple groups with different base
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Answer: limpa analysis advice
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53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
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53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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