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DESEq2
•
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0
votes
0
replies
11
views
Plot title for PCA in DESeq2
DESeq2
2 hours ago
AL
• 0
0
votes
3
replies
352
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 22 hours ago by
Michael Love
43k • written 3 days ago by
Marwan
• 0
1
vote
2
replies
976
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 7 days ago by
ATpoint
★ 4.7k • written 8 days ago by
ingrid.h
• 0
0
votes
1
reply
128
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 10 days ago by
Michael Love
43k • written 15 days ago by
Sahil
• 0
0
votes
3
replies
450
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 days ago by
980linnet
• 0 • written 16 days ago by
Guilherme
• 0
0
votes
2
replies
337
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 14 days ago by
Blair
• 0 • written 19 days ago by
A
• 0
0
votes
2
replies
306
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
19 days ago • updated 18 days ago
Martijn
• 0
0
votes
3
replies
354
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 19 days ago by
jodan
• 0 • written 27 days ago by
Quang NN
▴ 10
0
votes
1
reply
156
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 23 days ago by
Michael Love
43k • written 24 days ago by
Sim
• 0
2
votes
2
replies
430
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 25 days ago by
swbarnes2
★ 1.4k • written 28 days ago by
Nathan
• 0
0
votes
4
replies
929
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
27 days ago • updated 24 days ago
Quang NN
▴ 10
0
votes
2
replies
371
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
4 weeks ago • updated 28 days ago
Blandine
• 0
0
votes
5
replies
321
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 4 weeks ago by
georgeyu703
• 0
0
votes
4
replies
464
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
4 weeks ago
Quang NN
▴ 10
2
votes
5
replies
373
views
Differential variability modelling with vst() expression
limma
DESeq2
written 6 weeks ago by
jtsy6383
• 0
0
votes
3
replies
522
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 6 weeks ago by
sindhuri
• 0
2
votes
9
replies
910
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
6 weeks ago • updated 4 weeks ago
Quang NN
▴ 10
1
vote
1
reply
361
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
199
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
380
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 7 weeks ago by
Michael Love
43k • written 8 weeks ago by
Jimmy Mak
• 0
2
votes
1
reply
378
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 7 weeks ago by
Michael Love
43k • written 8 weeks ago by
KR
• 0
0
votes
2
replies
338
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
7 weeks ago
Kucsera
• 0
1
vote
1
reply
395
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 9 weeks ago by
Michael Love
43k • written 10 weeks ago by
txema.heredia
• 0
1
vote
9
replies
889
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 9 weeks ago by
anna.cot.anna.cot
▴ 30
4
votes
2
replies
444
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 9 weeks ago by
ATpoint
★ 4.7k • written 10 weeks ago by
bbao
▴ 10
1
vote
5
replies
617
views
Deseq2 Design
RNASeq
DESeq2
updated 9 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
pm_25
• 0
0
votes
5
replies
581
views
p value is 0, padj is 0
DESeq2
10 weeks ago
Wirayatida
• 0
1
vote
2
replies
563
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
10 weeks ago
georgii.vdovin
• 0
0
votes
7
replies
895
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 10 weeks ago by
txema.heredia
• 0 • written 10 weeks ago by
fjrsa
• 0
0
votes
1
reply
323
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 11 weeks ago by
bhandary.8590
▴ 20
0
votes
3
replies
459
views
DESeq2 - Comparing Comparisons
DESeq2
updated 10 weeks ago by
James W. MacDonald
68k • written 11 weeks ago by
sk
• 0
0
votes
4
replies
594
views
lfcShrink and alpha value
lfcShrink
DESeq2
12 weeks ago • updated 11 weeks ago
cropero
• 0
2
votes
1
reply
346
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
254
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
295
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
12 weeks ago
Anna
• 0
1
vote
2
replies
594
views
Deseq2 res Function
DESeq2
updated 12 weeks ago by
James W. MacDonald
68k • written 3 months ago by
sap275
▴ 10
0
votes
4
replies
483
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
3 months ago
NB
• 0
0
votes
5
replies
510
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
maripane
• 0
0
votes
1
reply
287
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
rj1435
• 0
1
vote
2
replies
348
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
3 months ago
Denise
• 0
0
votes
1
reply
198
views
eRNAs count
RNASeq
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
Irene
• 0
0
votes
1
reply
444
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
303
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
282
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
702
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 26 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
430
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 3 months ago by
ballackselma
• 0
4
votes
5
replies
764
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
3 months ago
LuciaNhu
• 0
0
votes
1
reply
465
views
Average expression of genes across replicates
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
James
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 It is correct to use interaction term for patient variability?
by
Bradley
• 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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