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DEseq2
•
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1
vote
2
replies
949
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 3 days ago by
ATpoint
★ 4.7k • written 4 days ago by
ingrid.h
• 0
0
votes
1
reply
117
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 7 days ago by
Michael Love
43k • written 11 days ago by
Sahil
• 0
0
votes
3
replies
425
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 7 days ago by
980linnet
• 0 • written 12 days ago by
Guilherme
• 0
0
votes
2
replies
330
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 days ago by
Blair
• 0 • written 15 days ago by
A
• 0
0
votes
2
replies
300
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
15 days ago • updated 14 days ago
Martijn
• 0
0
votes
3
replies
338
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 15 days ago by
jodan
• 0 • written 23 days ago by
Quang NN
▴ 10
0
votes
1
reply
144
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 20 days ago by
Michael Love
43k • written 21 days ago by
Sim
• 0
2
votes
2
replies
420
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 21 days ago by
swbarnes2
★ 1.4k • written 25 days ago by
Nathan
• 0
0
votes
4
replies
923
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
23 days ago • updated 21 days ago
Quang NN
▴ 10
0
votes
2
replies
345
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
27 days ago • updated 25 days ago
Blandine
• 0
0
votes
5
replies
303
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 27 days ago by
georgeyu703
• 0
0
votes
4
replies
435
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
29 days ago • updated 27 days ago
Quang NN
▴ 10
2
votes
5
replies
357
views
Differential variability modelling with vst() expression
limma
DESeq2
written 5 weeks ago by
jtsy6383
• 0
0
votes
3
replies
510
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 5 weeks ago by
sindhuri
• 0
2
votes
9
replies
888
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
5 weeks ago • updated 29 days ago
Quang NN
▴ 10
1
vote
1
reply
351
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
muhammadsohailraza
• 0
0
votes
1
reply
195
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 6 weeks ago by
swbarnes2
★ 1.4k • written 6 weeks ago by
natalievillafranca
• 0
0
votes
1
reply
378
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 8 weeks ago by
Jimmy Mak
• 0
2
votes
1
reply
371
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 6 weeks ago by
Michael Love
43k • written 7 weeks ago by
KR
• 0
0
votes
2
replies
330
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
7 weeks ago
Kucsera
• 0
1
vote
1
reply
391
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 8 weeks ago by
Michael Love
43k • written 9 weeks ago by
txema.heredia
• 0
1
vote
9
replies
868
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 8 weeks ago by
anna.cot.anna.cot
▴ 30
4
votes
2
replies
439
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 9 weeks ago by
ATpoint
★ 4.7k • written 9 weeks ago by
bbao
▴ 10
1
vote
5
replies
610
views
Deseq2 Design
RNASeq
DESeq2
updated 9 weeks ago by
James W. MacDonald
68k • written 9 weeks ago by
pm_25
• 0
0
votes
5
replies
571
views
p value is 0, padj is 0
DESeq2
9 weeks ago
Wirayatida
• 0
1
vote
2
replies
554
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
9 weeks ago
georgii.vdovin
• 0
0
votes
7
replies
882
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 9 weeks ago by
txema.heredia
• 0 • written 10 weeks ago by
fjrsa
• 0
0
votes
1
reply
316
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 10 weeks ago by
Michael Love
43k • written 10 weeks ago by
bhandary.8590
▴ 20
0
votes
3
replies
454
views
DESeq2 - Comparing Comparisons
DESeq2
updated 9 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
sk
• 0
0
votes
4
replies
583
views
lfcShrink and alpha value
lfcShrink
DESeq2
11 weeks ago • updated 10 weeks ago
cropero
• 0
2
votes
1
reply
342
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 11 weeks ago by
Michael Love
43k • written 12 weeks ago by
Nikita
• 0
0
votes
2
replies
249
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 11 weeks ago by
Michael Love
43k • written 11 weeks ago by
Sam
• 0
0
votes
2
replies
289
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
11 weeks ago
Anna
• 0
1
vote
2
replies
583
views
Deseq2 res Function
DESeq2
updated 12 weeks ago by
James W. MacDonald
68k • written 12 weeks ago by
sap275
▴ 10
0
votes
4
replies
479
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
12 weeks ago
NB
• 0
0
votes
5
replies
498
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 12 weeks ago by
Michael Love
43k • written 12 weeks ago by
maripane
• 0
0
votes
1
reply
284
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 12 weeks ago by
James W. MacDonald
68k • written 12 weeks ago by
rj1435
• 0
1
vote
2
replies
347
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
3 months ago • updated 12 weeks ago
Denise
• 0
0
votes
1
reply
196
views
eRNAs count
RNASeq
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
Irene
• 0
0
votes
1
reply
441
views
DESeq2 rerun returns different results
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
wl1111
• 0
0
votes
1
reply
296
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Jason
• 0
0
votes
1
reply
276
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 3 months ago by
Guido Hooiveld
★ 4.1k • written 3 months ago by
Najla Abassi
• 0
2
votes
2
replies
693
views
Handling biological replicates in DESeq2
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
sk
• 0
5
votes
2
replies
26k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 23 days ago by
fuqichen1
• 0 • written 6.1 years ago by
aishu.jp
▴ 30
1
vote
6
replies
1.1k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 3 months ago by
Michael Love
43k • written 3 months ago by
nramakr
▴ 10
0
votes
2
replies
425
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 3 months ago by
ballackselma
• 0
4
votes
5
replies
752
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
3 months ago
LuciaNhu
• 0
0
votes
1
reply
462
views
Average expression of genes across replicates
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
James
• 0
0
votes
0
replies
181
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
3 months ago
info
▴ 10
0
votes
10
replies
1.5k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
3 months ago
Denise
• 0
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A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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