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RnaSeq
•
reset
0
votes
2
replies
153
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
1 day ago • updated 6 hours ago
Marwan
• 0
1
vote
2
replies
963
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 5 days ago by
ATpoint
★ 4.7k • written 5 days ago by
ingrid.h
• 0
0
votes
1
reply
120
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 8 days ago by
Michael Love
43k • written 12 days ago by
Sahil
• 0
0
votes
3
replies
340
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 16 days ago by
jodan
• 0 • written 25 days ago by
Quang NN
▴ 10
0
votes
1
reply
147
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 21 days ago by
Michael Love
43k • written 22 days ago by
Sim
• 0
0
votes
2
replies
499
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
22 days ago • updated 5 days ago
ingrid.h
• 0
0
votes
4
replies
925
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
25 days ago • updated 22 days ago
Quang NN
▴ 10
0
votes
3
replies
514
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 5 weeks ago by
sindhuri
• 0
4
votes
2
replies
440
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
611
views
Deseq2 Design
RNASeq
DESeq2
updated 9 weeks ago by
James W. MacDonald
68k • written 9 weeks ago by
pm_25
• 0
0
votes
2
replies
515
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 10 weeks ago by
Gordon Smyth
52k • written 10 weeks ago by
Lina
▴ 10
0
votes
1
reply
245
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 12 weeks ago by
ATpoint
★ 4.7k • written 12 weeks ago by
siobhan.dietz
• 0
0
votes
5
replies
586
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 3 months ago by
Kent
• 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
1
vote
8
replies
1.3k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma
voom
RNASeq
edgeR
Microarray
written 3 months ago by
Adam Marstrand
• 0
0
votes
0
replies
183
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
3 months ago
brayas13
• 0
3
votes
11
replies
905
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 4 months ago by
bioshot.com
• 0
2
votes
4
replies
504
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
4 months ago
jihoon.kim.1495
▴ 10
1
vote
1
reply
463
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Caroline
• 0
1
vote
2
replies
559
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Ben
▴ 10
0
votes
3
replies
548
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
4 months ago
Travis
• 0
0
votes
5
replies
1.9k
views
DESeq2 Multi-factor design not full rank
RNASeq
DESeq2
written 3.8 years ago by
jehimi
• 0
0
votes
2
replies
1.0k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq
DESeq2
updated 5 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Shwetal
• 0
3
votes
5
replies
1.3k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2
RNAseq
DifferentialExpression
updated 6 months ago by
swbarnes2
★ 1.4k • written 6 months ago by
BioNovice247
• 0
2
votes
3
replies
685
views
RUV - Does my data need further normalisation?
EDASeq
plotRLE
RNAseq
6 months ago
BioinfGuru
▴ 70
3
votes
6
replies
898
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
written 6 months ago by
MedocRafael
• 0
4
votes
3
replies
1.3k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
written 7 months ago by
mila
▴ 10
0
votes
3
replies
651
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 7 months ago by
ATpoint
★ 4.7k • written 7 months ago by
Mark
• 0
1
vote
4
replies
1.6k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
7 months ago
Lucy
▴ 60
0
votes
4
replies
687
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 7 months ago by
Shaozhen
• 0
0
votes
0
replies
419
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
7 months ago
JG13
• 0
0
votes
1
reply
431
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
cbio
• 0
1
vote
9
replies
1.9k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
adrip
▴ 10
1
vote
3
replies
663
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
Ben
▴ 50
2
votes
2
replies
715
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 8 months ago by
jessica.mcclintock
▴ 10 • written 9 months ago by
ttt
• 0
0
votes
6
replies
1.5k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
9 months ago • updated 8 months ago
atan
• 0
3
votes
2
replies
775
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
9 months ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
363
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
9 months ago
Bibi
• 0
10
votes
11
replies
2.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 9 months ago by
Sara
• 0 • written 7.5 years ago by
Sylvain Foisy
▴ 80
1
vote
3
replies
738
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
Ashley
• 0
0
votes
3
replies
944
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 9 months ago by
ATpoint
★ 4.7k • written 9 months ago by
james.zhang20
• 0
0
votes
1
reply
599
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
kcarey
• 0
0
votes
2
replies
517
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 10 months ago by
taur.vil
• 0
0
votes
2
replies
715
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
10 months ago
catv
• 0
5
votes
3
replies
1.1k
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 months ago by
Gordon Smyth
52k • written 10 months ago by
Shaimaa Gamal
• 0
0
votes
1
reply
756
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
09191919
• 0
0
votes
1
reply
631
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 10 months ago by
ATpoint
★ 4.7k • written 10 months ago by
Merav
• 0
0
votes
2
replies
1.3k
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
11 months ago
kcarey
• 0
2
votes
2
replies
589
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
11 months ago
Sabiha
▴ 20
0
votes
2
replies
1.8k
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
11 months ago
kcarey
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to formulate 2 factor nested design in DESeq2
by
Mariane
• 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data
by
gaye.yilmaz
• 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes
by
James W. MacDonald
68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2
by
Marwan
• 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Answer: Differential variance analysis - can i use deseq2
by
Michael Love
43k
We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
Votes
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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