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rnaseq
•
reset
0
votes
0
replies
3
views
scRNA seq data trained model use on bulk RNA-seq data for prediction
RNASeq
scRNAseq
10 minutes ago
Bibi
• 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
1
vote
3
replies
245
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
Ashley
• 0
0
votes
3
replies
224
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
james.zhang20
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 24 days ago by
Michael Love
42k • written 24 days ago by
kcarey
• 0
0
votes
2
replies
191
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 26 days ago by
taur.vil
• 0
0
votes
2
replies
239
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
29 days ago • updated 27 days ago
catv
• 0
5
votes
3
replies
310
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
0
votes
1
reply
128
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
1
reply
154
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Merav
• 0
0
votes
2
replies
269
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 weeks ago
kcarey
• 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
9 weeks ago
Sabiha
▴ 20
0
votes
2
replies
315
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
9 weeks ago
kcarey
• 0
1
vote
4
replies
332
views
DESeq2 Replicates
DESeq2
RNASeq
10 weeks ago
kcarey
• 0
1
vote
3
replies
388
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 10 weeks ago by
swbarnes2
★ 1.4k • written 11 weeks ago by
sap275
▴ 10
0
votes
4
replies
325
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago
mperalc
• 0
0
votes
2
replies
346
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
ryann
• 0
3
votes
5
replies
670
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
2
votes
1
reply
279
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 11 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 10
3
votes
6
replies
591
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
3 months ago • updated 12 weeks ago
boczniak767
▴ 720
0
votes
0
replies
242
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
2
votes
2
replies
438
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
3 months ago
jackafiore
• 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
0
votes
4
replies
440
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
3 months ago
candacenewcome
• 0
1
vote
3
replies
359
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
3 months ago
island
• 0
1
vote
3
replies
626
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 3 months ago by
georgii.vdovin
• 0
0
votes
1
reply
260
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 3 months ago by
Ram
▴ 210 • written 3 months ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
650
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
4
votes
6
replies
643
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
328
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
547
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 4 months ago by
Fayrouz
• 0
0
votes
1
reply
288
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
4 months ago
WS
• 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Bo
• 0
1
vote
2
replies
498
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
5 months ago • updated 4 months ago
Sabiha
▴ 20
1
vote
2
replies
469
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
5 months ago
drewhaydensteele
• 0
7
votes
2
replies
864
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
3
replies
481
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
1
vote
1
reply
394
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 5 months ago by
Michael Love
42k • written 5 months ago by
pl23
• 0
2
votes
3
replies
523
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
5 months ago
Karthik
• 0
2
votes
2
replies
438
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
6 months ago • updated 5 months ago
Manthos
• 0
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
6 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
462
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 6 months ago by
Michael Love
42k • written 7 months ago by
Sean
• 0
0
votes
2
replies
564
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 6 months ago by
Leonardo Collado Torres
★ 1.0k • written 6 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.6 years ago by
bharata1803
▴ 60
1
vote
4
replies
661
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
6 months ago
Wending
• 0
0
votes
0
replies
375
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
6 months ago
mch
• 0
4
votes
2
replies
676
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
920
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
352
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
7 months ago
Sara
• 0
0
votes
2
replies
663
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
7 months ago • updated 6 months ago
Karthik
• 0
50 results • Page
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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
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Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
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Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
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