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Showing :
RNASeqData
•
reset
3
votes
6
replies
851
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 4 weeks ago by
Ahmed Salah
• 0
0
votes
2
replies
468
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 23 days ago by
MarcHintz99
• 0 • written 3 months ago by
Rui
• 0
3
votes
13
replies
2.2k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 14 months ago by
bioshot.com
• 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 6 months ago by
Christian
▴ 20
0
votes
1
reply
781
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
Cosmic
• 0
1
vote
1
reply
449
views
Merging annotation with differential expression output
annotation
RNASeqData
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
AL
• 0
0
votes
3
replies
1.0k
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Marwan
• 0
0
votes
0
replies
369
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing
RNASeqData
DEXSeq
10 months ago
cftattersfield
• 0
0
votes
5
replies
752
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 11 months ago by
georgeyu703
• 0
0
votes
1
reply
482
views
Correlation between gene clusters
genomes
RNASeqData
written 11 months ago by
Le
• 0
0
votes
2
replies
736
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
11 months ago
gingergeiger22
• 0
2
votes
1
reply
745
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 11 months ago by
Michael Love
43k • written 12 months ago by
KR
• 0
0
votes
1
reply
652
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 12 months ago by
O'Brien
• 0 • written 12 months ago by
Noor
• 0
2
votes
1
reply
751
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 12 months ago by
Michael Love
43k • written 13 months ago by
Nikita
• 0
0
votes
4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs
edgeR
RNASeqData
14 months ago
Philippine
• 0
0
votes
2
replies
834
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 14 months ago by
Aleksandra
• 0
1
vote
1
reply
996
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 14 months ago by
Lluís Revilla Sancho
▴ 760 • written 14 months ago by
Nasim
• 0
1
vote
1
reply
719
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Pimpa
• 0
1
vote
1
reply
882
views
Help with design matrix for RNA-seq data using edgeR
edgeR
RNASeqData
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
erik.burchard
• 0
1
vote
2
replies
3.3k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 15 months ago by
b8177
• 0
1
vote
2
replies
712
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2
RNASeqData
apeglm
16 months ago
Gordon
• 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
Mark
• 0
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 17 months ago by
Shaozhen
• 0
1
vote
3
replies
2.0k
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
18 months ago
Tanvi
• 0
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Ben
▴ 50
0
votes
1
reply
660
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData
DESeq2
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
ZhuYi
• 0
0
votes
1
reply
752
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
updated 15 months ago by
jg
▴ 20 • written 19 months ago by
Shaimaa Gamal
• 0
0
votes
1
reply
664
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
z_bahari
• 0
0
votes
1
reply
678
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Leyre
• 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 22 months ago by
Michael Love
43k • written 22 months ago by
sap275
▴ 10
0
votes
0
replies
779
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
22 months ago
Abril
• 0
1
vote
2
replies
2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 2.6 years ago by
informatician
• 0
1
vote
3
replies
1.2k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
23 months ago
island
• 0
0
votes
2
replies
854
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus
RNASeqData
23 months ago
Diana
• 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
Ömür Koray
• 0
5
votes
6
replies
1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
23 months ago
Shaimaa Gamal
• 0
1
vote
1
reply
988
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 24 months ago by
ATpoint
★ 5.0k • written 2.0 years ago by
kubracelikbas4
• 0
0
votes
2
replies
1.3k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
2.0 years ago
Luca
• 0
0
votes
1
reply
1.7k
views
Interaction terms in DESeq2
RNASeqData
RnaSeqSampleSize
DESeq2
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Mimi
• 0
1
vote
2
replies
1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
2.1 years ago
drewhaydensteele
• 0
1
vote
1
reply
971
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
kaurprab
• 0
1
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
2.1 years ago • updated 24 months ago
Levi
• 0
0
votes
3
replies
2.7k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
2.1 years ago
Oenone
• 0
3
votes
4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
2.1 years ago
pl23
• 0
0
votes
1
reply
803
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Pez
▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
2.1 years ago
Manthos
• 0
0
votes
1
reply
911
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 2.1 years ago by
Wolfgang Huber
★ 13k • written 2.1 years ago by
meroy
• 0
0
votes
2
replies
1.0k
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData
DESeq2
2.1 years ago
Ben
▴ 10
0
votes
2
replies
2.7k
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
2.1 years ago
RHEA
• 0
2
votes
3
replies
2.7k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
Sam
• 0
152 results • Page
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Comment: nice 3D displays for PCA analysis
by
adam80haynes
• 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
• 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
• 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long?
by
ATpoint
★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Votes
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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