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RnaSeq
•
reset
0
votes
0
replies
23
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
23 hours ago • updated 21 hours ago
JAcky
• 0
2
votes
2
replies
66
views
Can't load UCSC transcript IDs
RNASeq
updated 6 days ago by
Guido Hooiveld
★ 3.3k • written 7 days ago by
becker.jemima
• 0
1
vote
2
replies
103
views
deseq2 lfc shrinkage with few DEGs
RNASeq
DESeq2
7 days ago
Victor
• 0
3
votes
3
replies
132
views
Nested analysis or Collapsed-replicate analysis?
RNASeq
DESeq2
updated 7 days ago by
Michael Love
37k • written 18 days ago by
giulia.lopatriello
• 0
0
votes
1
reply
77
views
lfc Shrinkage with multiple comparison groups
RNAseq
lfcShrinkage
DESeq2
updated 14 days ago by
ATpoint
★ 1.3k • written 15 days ago by
m.lorgen.06
• 0
0
votes
1
reply
55
views
Nested analysis or Collapsed-replicate analysis?
RNASeq
DESeq2
updated 17 days ago by
Michael Love
37k • written 18 days ago by
giulia.lopatriello
• 0
1
vote
1
reply
126
views
RNA-Seq normalization and batch effect removal
RNASeq
BatchEffect
DESeq2
updated 17 days ago by
Michael Love
37k • written 19 days ago by
Alexandre
• 0
0
votes
1
reply
64
views
NOIseq Probability column
RNAseq
RNASeqData
NOISeq
22 days ago • updated 11 days ago
Pratibha
• 0
3
votes
3
replies
167
views
Limma vs deseq2 results
limma
RNASeq
R
28 days ago • updated 26 days ago
k___
▴ 20
3
votes
3
replies
167
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 5 weeks ago by
Gordon Smyth
45k • written 5 weeks ago by
mohammedtoufiq91
▴ 10
3
votes
6
replies
308
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq
DESeq2
5 weeks ago
andrebolerbarros
▴ 10
0
votes
2
replies
229
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 7 weeks ago by
curiousmind007
• 0
1
vote
1
reply
117
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 5 weeks ago by
Gordon Smyth
45k • written 5 weeks ago by
margo
• 0
1
vote
2
replies
156
views
How to properly use DESeq2 for an experiment
ExperimentalDesign
RNASeq
DifferentialExpression
DESeq2
updated 6 weeks ago by
Michael Love
37k • written 6 weeks ago by
Aurélien
• 0
3
votes
11
replies
447
views
RNA-seq: compare two technical replicates
RNASeq
updated 7 weeks ago by
Gordon Smyth
45k • written 8 weeks ago by
Marianna
• 0
0
votes
2
replies
142
views
edgeR
rnaseq
edgeR
updated 9 weeks ago by
Gordon Smyth
45k • written 9 weeks ago by
edusbioinfo
• 0
0
votes
3
replies
176
views
Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 9 weeks ago by
swbarnes2
★ 1.1k • written 10 weeks ago by
theemperor79
• 0
5
votes
6
replies
316
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
10 weeks ago
Alan
• 0
0
votes
0
replies
92
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq
Clustering
cluster
WGCNA
10 weeks ago
chiwut.wong
• 0
0
votes
0
replies
82
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
11 weeks ago
OST
• 0
2
votes
4
replies
208
views
confused with tximport counts abundance using salmon input
RNASeq
tximport
11 weeks ago
Al90
• 0
0
votes
7
replies
349
views
DESeq2 on allelic reads
RNASeq
DifferentialExpression
DESeq2
updated 10 weeks ago by
Michael Love
37k • written 11 weeks ago by
Nayrouz
• 0
0
votes
1
reply
184
views
Rtracklayer
rtracklayer
RNASeq
gff
updated 12 weeks ago by
James W. MacDonald
60k • written 12 weeks ago by
edusbioinfo
• 0
0
votes
1
reply
150
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq
RNASeqData
limma
limmaGUI
updated 12 weeks ago by
Michael Love
37k • written 12 weeks ago by
sushimoto
• 0
0
votes
3
replies
184
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2
RNASeq
updated 3 months ago by
Michael Love
37k • written 3 months ago by
niko.fleischer
• 0
0
votes
2
replies
1.7k
views
DESeq2 counts distribution across both genes and samples
deseq2
rnaseq
updated 3 months ago by
BarryGutierrez
• 0 • written 5.8 years ago by
igor
▴ 40
0
votes
0
replies
120
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP
RNASeq
RNASeqData
3 months ago
treebig44
▴ 30
1
vote
0
replies
94
views
Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery
RNASeq
3 months ago
Liliian
• 0
0
votes
0
replies
212
views
Create a Gene Enrichment GO plot from goana output
goana
RNASeq
edgeR
RnaSeq
GO
3 months ago
Raito92
▴ 60
2
votes
2
replies
174
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS
PCA
RNASeq
MDS
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
Raito92
▴ 60
0
votes
4
replies
252
views
limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq
limma
3 months ago
danphillips28
• 0
0
votes
1
reply
164
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 3 months ago by
Robert Castelo
★ 2.9k • written 3 months ago by
jms2520
• 0
0
votes
1
reply
181
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE
RNASeq
DifferentialSplicingWorkflow
AlternativeSplicing
edgeR
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
zhaoqiao1027
• 0
4
votes
1
reply
224
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2
RNASeq
RNASeqData
updated 3 months ago by
Michael Love
37k • written 3 months ago by
treebig44
▴ 30
1
vote
1
reply
119
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 3 months ago by
Michael Love
37k • written 3 months ago by
treebig44
▴ 30
2
votes
6
replies
332
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2
RNASeq
RNASeqData
3 months ago
treebig44
▴ 30
0
votes
0
replies
118
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage
plot
RNASeq
goseq
updated 3 months ago by
Michael Love
37k • written 3 months ago by
m.glymenaki
• 0
2
votes
2
replies
208
views
Complex contrasts in limma
RNASeq
limma
DifferentialExpression
3 months ago
tcalvo
▴ 70
0
votes
2
replies
216
views
Differential expression in fixed windows
DESeq2
RNASeq
4 months ago
anatmela
• 0
2
votes
1
reply
224
views
DESeq2 handling of replicates
DESeq2
RNASeq
limma
updated 4 months ago by
Michael Love
37k • written 4 months ago by
Eyal
• 0
0
votes
1
reply
170
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 4 months ago by
Michael Love
37k • written 4 months ago by
István
• 0
0
votes
1
reply
216
views
95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2
RNASeq
updated 4 months ago by
ATpoint
★ 1.3k • written 4 months ago by
martin.kinisu
• 0
0
votes
1
reply
206
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb
RNASeq
updated 4 months ago by
James W. MacDonald
60k • written 4 months ago by
Jonas
• 0
0
votes
4
replies
362
views
How do you get averages of each group in Limma output
RNASeq
limma
4 months ago
Matthew
• 0
0
votes
6
replies
496
views
Performing simple pairwise comparisons in DESEQ2
edgeR
DEG
RNASeq
DESEQ2
updated 4 months ago by
Michael Love
37k • written 4 months ago by
Raito92
▴ 60
0
votes
4
replies
361
views
Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2
RNASeq
updated 5 months ago by
swbarnes2
★ 1.1k • written 5 months ago by
Matthew
• 0
0
votes
3
replies
405
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq
DESeq2
updated 5 months ago by
Basti
▴ 330 • written 5 months ago by
User000
• 0
0
votes
3
replies
469
views
using the goana function from edgeR
RNASeq
edgeR
GO
GOSemSim
updated 5 months ago by
Gordon Smyth
45k • written 5 months ago by
David Rengel
▴ 70
1
vote
2
replies
204
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 5 months ago by
Michael Love
37k • written 5 months ago by
Emma
• 0
0
votes
2
replies
222
views
Removing paired samples for DESeq2 analysis
RNASeq
DifferentialExpression
DESeq2
tcga
5 months ago
IamFrofro
• 0
50 results • Page
1 of 1
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Replies
Comment: Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelih
by
ATpoint
★ 1.3k
Would you mind reading the vignette towards how the LRT works: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2…
Comment: cellCounts() function floating point error
by
Yang Liao
▴ 340
Thanks for the report but the error cannot be reproduced. We tested `Rsubread` 2.10.3 in `R` 4.2.0 and `Bioconductor` 3.15, and `cellCounts…
Comment: rtracklayer export GRangesList as gtf and change attributes
by
James
• 0
I have found a way to export a GTF so that the 3rd column no longer lists **sequence_feature** but instead lists the feature, such as **exo…
Comment: Using Age or other numerical variable to model expression in deseq2
by
swbarnes2
★ 1.1k
You can import age and not make it a factor.
Comment: Using Age or other numerical variable to model expression in deseq2
by
krushnach80
• 0
"Why is that" no as an example i was citing that.."certainly don't want to make the interaction between the nuisance variable and your vari…
Votes
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
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