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RNASeqData
•
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0
votes
0
replies
639
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Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData
RNASeq
3.5 years ago
Pang
• 0
0
votes
1
reply
1.1k
views
I have a query regarding differential gene expression using limma-voom.
RNASeqData
DESeq2
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
btadfaramin
• 0
1
vote
7
replies
3.0k
views
DESeqDataSetFromMatrix error
BiocGenerics
DESeq2
DEGreport
RNASeqData
DEG
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Diya
• 0
2
votes
9
replies
4.3k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
3.6 years ago
Peipei
• 0
1
vote
5
replies
1.9k
views
Error in DEseq
DEseq
RNASeqData
updated 3.6 years ago by
ATpoint
★ 5.0k • written 3.6 years ago by
Sanatan
• 0
1
vote
1
reply
1.2k
views
NOIseq Probability column
RNAseq
RNASeqData
NOISeq
3.7 years ago • updated 3.6 years ago
Pratibha
▴ 10
5
votes
4
replies
2.8k
views
How to formulate 2 factor nested design in DESeq2
nested_design
RNASeqData
DESeq2
updated 11 months ago by
Mariane
• 0 • written 3.7 years ago by
JK Kim
▴ 30
0
votes
2
replies
2.4k
views
How to run vst transformation
RNASeqData
vst
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
sropri
• 0
2
votes
3
replies
2.0k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
3.7 years ago
Maka
• 0
0
votes
5
replies
3.5k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
3.8 years ago • updated 3.7 years ago
priyanka.m
• 0
22
votes
15
replies
12k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 2.2 years ago by
Marie
▴ 10 • written 3.8 years ago by
Dina
▴ 50
0
votes
2
replies
1.6k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData
DESeq2
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
treebig44
▴ 40
3
votes
2
replies
1.8k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
3.8 years ago • updated 3.7 years ago
Dakarai
▴ 10
0
votes
1
reply
1.3k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq
RNASeqData
limma
limmaGUI
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
sushimoto
• 0
0
votes
2
replies
2.2k
views
lncRNA Genes in a Dataset
ncRNAtools
RNASeqData
3.8 years ago
sushimoto
• 0
0
votes
0
replies
879
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR
ExpressionData
RNASeqData
3.8 years ago
Mafalda
• 0
1
vote
4
replies
1.6k
views
lncRNA Differential Expression Analysis
DESeq2
limma
RNASeqData
3.8 years ago
sushimoto
• 0
0
votes
0
replies
1.1k
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP
RNASeq
RNASeqData
3.8 years ago
treebig44
▴ 40
0
votes
0
replies
1.3k
views
high number of reads mapped to too many loci
RNASeqData
3.8 years ago
vasa.broz
• 0
0
votes
1
reply
1.2k
views
HSMMSingleCell metadata
ExperimentHubData
ExpressionData
CellDataSet
RNASeqData
3.9 years ago
karl.stamm
▴ 10
4
votes
1
reply
3.9k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2
RNASeq
RNASeqData
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
treebig44
▴ 40
1
vote
1
reply
1.0k
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 3.9 years ago by
Michael Love
43k • written 3.9 years ago by
treebig44
▴ 40
4
votes
6
replies
13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2
RNASeq
RNASeqData
3.9 years ago
treebig44
▴ 40
1
vote
1
reply
4.2k
views
Limma interaction term
RNASeqData
limma
DifferentialExpression
updated 3.9 years ago by
Gordon Smyth
53k • written 3.9 years ago by
bageerathan.v
• 0
1
vote
2
replies
1.5k
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
3.9 years ago • updated 3.8 years ago
m.glymenaki
• 0
1
vote
1
reply
1.3k
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 3.9 years ago by
Gordon Smyth
53k • written 3.9 years ago by
vikycairoli
• 0
4
votes
3
replies
2.1k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2
idep
RNASeqData
updated 3.9 years ago by
swbarnes2
★ 1.4k • written 3.9 years ago by
student2
▴ 10
0
votes
2
replies
1.3k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR
DEGs
DESEQ2
RNASeqData
4.0 years ago
Raito92
▴ 60
0
votes
1
reply
2.2k
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig
RNASeqData
4.0 years ago
bas_work
▴ 30
1
vote
1
reply
2.2k
views
Help understanding edgeR code for doing exactTest
exacttest
RNASeqData
edgeR
diffGeneAnalysis
updated 4.3 years ago by
Gordon Smyth
53k • written 4.3 years ago by
Julia
• 0
2
votes
4
replies
1.9k
views
DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData
DESeq2
4.4 years ago
khaveh
▴ 10
0
votes
2
replies
1.2k
views
Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
4.5 years ago
szomolay
• 0
0
votes
1
reply
1.1k
views
Query regarding WGCNA module formation
WGCNA
RNAseq
RNASeqData
updated 4.7 years ago by
Lluís Revilla Sancho
▴ 760 • written 4.7 years ago by
abhisek001
• 0
0
votes
3
replies
1.5k
views
Contrasting LogFCs in DESeq2
DESeq2
RNASeqData
updated 4.7 years ago by
swbarnes2
★ 1.4k • written 4.7 years ago by
GlycineMax
• 0
0
votes
1
reply
1.3k
views
t.fit stops in masigpro while running RNA seq data
RNASeqData
maSigPro
4.8 years ago • updated 4.7 years ago
subashika
• 0
8
votes
2
replies
11k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
4.8 years ago
paty
▴ 60
1
vote
3
replies
3.5k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData
RNASeq
RNASeqR
4.8 years ago
dantasezequiel1
• 0
1
vote
15
replies
4.0k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
4.8 years ago
demisa
• 0
0
votes
6
replies
1.9k
views
while doing co-expression network analysis, I am getting an error
RNASeqData
4.8 years ago
Rishav
▴ 20
2
votes
8
replies
4.0k
views
While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 4.8 years ago by
Gordon Smyth
53k • written 4.8 years ago by
Rishav
▴ 20
3
votes
4
replies
2.4k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
4.8 years ago
hgalmoore
• 0
7
votes
4
replies
18k
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
updated 4.1 years ago by
BioNovice247
• 0 • written 4.9 years ago by
Emma
▴ 20
3
votes
2
replies
1.4k
views
Why some statistically differently expressed genes are not DEGs?
RNASeqData
DEGreport
edgeR
4.9 years ago
Wuschel
▴ 10
1
vote
6
replies
2.2k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData
DESeq2
rnaseqGene
5.0 years ago
Seaweed
• 0
9
votes
5
replies
5.5k
views
Normalise to a housekeeping gene in DESEq2
DESeq2
housekeeping
R
RNASeqData
5.2 years ago
ecg1g15
▴ 30
3
votes
6
replies
1.9k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2
RNASeqData
DifferentialExpression
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Ben
▴ 50
2
votes
4
replies
3.8k
views
Compare 3 RNASeq groups with no control in DESeq2
anova
RNASeqData
tukeyTest
DESeq2
5.2 years ago
ecg1g15
▴ 30
0
votes
1
reply
932
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData
GenomeInfoDb
updated 5.2 years ago by
Kevin Blighe
★ 4.0k • written 5.2 years ago by
G.G.H.T.
• 0
0
votes
3
replies
9.7k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor
RNASeqData
DESeq2
Rsubread
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
Rafael
• 0
0
votes
1
reply
1.3k
views
RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2
multiple factor design
rnaseqdata
updated 9.8 years ago by
Michael Love
43k • written 9.8 years ago by
Dimitris Polychronopoulos
▴ 80
152 results • Page
3 of 4
Recent ...
Replies
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice
by
Gordon Smyth
53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency)
by
shepherl
4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
Votes
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
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