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RNASeqData
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588
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 7 weeks ago by
ATpoint
★ 4.8k • written 7 weeks ago by
Cosmic
• 0
1
vote
1
reply
267
views
Merging annotation with differential expression output
annotation
RNASeqData
updated 7 weeks ago by
James W. MacDonald
68k • written 7 weeks ago by
AL
• 0
0
votes
3
replies
656
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 12 weeks ago by
Michael Love
43k • written 12 weeks ago by
Marwan
• 0
0
votes
0
replies
162
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
3 months ago
cftattersfield
• 0
0
votes
5
replies
453
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 3 months ago by
georgeyu703
• 0
0
votes
1
reply
300
views
Correlation between gene clusters
genomes
RNASeqData
written 4 months ago by
Le
• 0
0
votes
2
replies
436
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
4 months ago
gingergeiger22
• 0
2
votes
1
reply
480
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 4 months ago by
Michael Love
43k • written 4 months ago by
KR
• 0
0
votes
1
reply
341
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 4 months ago by
O'Brien
• 0 • written 4 months ago by
Noor
• 0
2
votes
1
reply
511
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 5 months ago by
Michael Love
43k • written 5 months ago by
Nikita
• 0
0
votes
4
replies
828
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs
edgeR
RNASeqData
6 months ago
Philippine
• 0
0
votes
2
replies
539
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 6 months ago by
Aleksandra
• 0
3
votes
11
replies
1.1k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 7 months ago by
bioshot.com
• 0
1
vote
1
reply
657
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 7 months ago by
Lluís Revilla Sancho
▴ 760 • written 7 months ago by
Nasim
• 0
1
vote
1
reply
402
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 7 months ago by
ATpoint
★ 4.8k • written 7 months ago by
Pimpa
• 0
1
vote
1
reply
677
views
Help with design matrix for RNA-seq data using edgeR
edgeR
RNASeqData
updated 8 months ago by
Gordon Smyth
52k • written 8 months ago by
erik.burchard
• 0
1
vote
2
replies
2.6k
views
How to use compareCluster in ClusterProfiler?
RNASeqData
GSEA
clusterProfiler
written 8 months ago by
b8177
• 0
1
vote
2
replies
496
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2
RNASeqData
apeglm
8 months ago
Gordon
• 0
0
votes
3
replies
767
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 9 months ago by
ATpoint
★ 4.8k • written 9 months ago by
Mark
• 0
0
votes
4
replies
829
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 10 months ago by
Shaozhen
• 0
1
vote
3
replies
1.6k
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
11 months ago
Tanvi
• 0
1
vote
3
replies
790
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Ben
▴ 50
0
votes
1
reply
494
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData
DESeq2
DifferentialExpression
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
ZhuYi
• 0
0
votes
1
reply
497
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
updated 8 months ago by
jg
▴ 20 • written 12 months ago by
Shaimaa Gamal
• 0
0
votes
1
reply
508
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 12 months ago by
Gordon Smyth
52k • written 12 months ago by
z_bahari
• 0
0
votes
1
reply
480
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Leyre
• 0
3
votes
5
replies
1.4k
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 14 months ago by
Michael Love
43k • written 15 months ago by
sap275
▴ 10
0
votes
0
replies
639
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
15 months ago
Abril
• 0
1
vote
2
replies
2.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 2.0 years ago by
informatician
• 0
1
vote
3
replies
951
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
15 months ago
island
• 0
0
votes
2
replies
638
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus
RNASeqData
15 months ago
Diana
• 0
0
votes
1
reply
961
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 16 months ago by
ATpoint
★ 4.8k • written 16 months ago by
Ömür Koray
• 0
5
votes
6
replies
1.2k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
16 months ago
Shaimaa Gamal
• 0
1
vote
1
reply
801
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 17 months ago by
ATpoint
★ 4.8k • written 17 months ago by
kubracelikbas4
• 0
0
votes
2
replies
971
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
17 months ago
Luca
• 0
0
votes
1
reply
1.4k
views
Interaction terms in DESeq2
RNASeqData
RnaSeqSampleSize
DESeq2
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Mimi
• 0
1
vote
2
replies
990
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
17 months ago
drewhaydensteele
• 0
1
vote
1
reply
800
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 17 months ago by
ATpoint
★ 4.8k • written 17 months ago by
kaurprab
• 0
1
vote
2
replies
1.6k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
17 months ago • updated 16 months ago
Levi
• 0
0
votes
3
replies
2.3k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
17 months ago
Oenone
• 0
3
votes
4
replies
1.2k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
18 months ago
pl23
• 0
0
votes
1
reply
652
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
Pez
▴ 10
2
votes
2
replies
864
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
18 months ago
Manthos
• 0
0
votes
1
reply
770
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 18 months ago by
Wolfgang Huber
★ 13k • written 18 months ago by
meroy
• 0
0
votes
2
replies
814
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData
DESeq2
18 months ago
Ben
▴ 10
0
votes
2
replies
2.4k
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
18 months ago
RHEA
• 0
2
votes
3
replies
2.3k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 19 months ago by
swbarnes2
★ 1.4k • written 19 months ago by
Sam
• 0
1
vote
1
reply
906
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
fuqichen1
• 0
1
vote
7
replies
1.5k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 17 months ago by
Gordon Smyth
52k • written 19 months ago by
Gimena
• 0
0
votes
1
reply
828
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 19 months ago by
Basti
▴ 780 • written 19 months ago by
Luke
• 0
50 results • Page
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Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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