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RNASeqData
•
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0
votes
0
replies
53
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
3 days ago
Shaimaa Gamal
• 0
0
votes
1
reply
178
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
z_bahari
• 0
0
votes
1
reply
128
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Leyre
• 0
3
votes
5
replies
671
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 12 weeks ago by
sap275
▴ 10
0
votes
0
replies
243
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 12 months ago by
informatician
• 0
1
vote
3
replies
361
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
3 months ago
island
• 0
0
votes
2
replies
292
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus
RNASeqData
3 months ago
Diana
• 0
0
votes
1
reply
334
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Ömür Koray
• 0
5
votes
6
replies
606
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
4 months ago • updated 3 months ago
Shaimaa Gamal
• 0
1
vote
1
reply
420
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
kubracelikbas4
• 0
0
votes
2
replies
379
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
5 months ago
Luca
• 0
0
votes
1
reply
363
views
Interaction terms in DESeq2
RNASeqData
RnaSeqSampleSize
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
Mimi
• 0
1
vote
2
replies
471
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
5 months ago
drewhaydensteele
• 0
1
vote
1
reply
354
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
kaurprab
• 0
1
vote
2
replies
700
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
0
votes
3
replies
735
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
5 months ago
Oenone
• 0
3
votes
4
replies
560
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
0
votes
1
reply
372
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 6 months ago by
Michael Love
42k • written 6 months ago by
Pez
▴ 10
2
votes
2
replies
440
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
6 months ago
Manthos
• 0
0
votes
1
reply
411
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 6 months ago by
Wolfgang Huber
★ 13k • written 6 months ago by
meroy
• 0
0
votes
2
replies
473
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData
DESeq2
6 months ago
Ben
• 0
0
votes
2
replies
751
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
6 months ago
RHEA
• 0
2
votes
3
replies
857
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 6 months ago by
swbarnes2
★ 1.4k • written 6 months ago by
Sam
• 0
1
vote
1
reply
446
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
fuqichen1
• 0
1
vote
7
replies
881
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 5 months ago by
Gordon Smyth
50k • written 7 months ago by
Gimena
• 0
0
votes
1
reply
420
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 7 months ago by
Basti
▴ 780 • written 7 months ago by
Luke
• 0
2
votes
4
replies
727
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
7 months ago
Shihui
• 0
0
votes
4
replies
689
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
sohail.mbio
▴ 10
3
votes
3
replies
1.3k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
8 months ago
Ethan Nguyen
• 0
0
votes
1
reply
683
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
khaserdene99
• 0
0
votes
2
replies
535
views
RSubread DESeq2
RNASeqData
DifferentialExpression
DESeq2
8 months ago
Beyza
• 0
1
vote
1
reply
477
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
jg0428
• 0
0
votes
0
replies
342
views
How to use erccdashboard with erccmix="Single" design
RNASeqData
erccdashboard
8 months ago
adi.rotem
• 0
0
votes
1
reply
515
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Sep
• 0
0
votes
1
reply
533
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData
DEGseq
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
sybyun419
• 0
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
D-Bug
▴ 10
0
votes
2
replies
1.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
vitoriastavis
• 0
0
votes
2
replies
960
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData
DESeq2
9 months ago
Marina
• 0
1
vote
2
replies
1.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 9 months ago by
k.vitting.seerup
▴ 120 • written 9 months ago by
elva.gypsophila
▴ 10
0
votes
6
replies
810
views
Questionable limma results for differential expression on RNA-seq
RNASeqData
DifferentialExpression
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
gld-bioinf
• 0
1
vote
2
replies
541
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
mohammad.hossein.banabazi
• 0
0
votes
0
replies
344
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
10 months ago
sonal
• 0
1
vote
9
replies
912
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Matteo
• 0
0
votes
0
replies
561
views
News:
Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor
Network
RNASeqData
SystemsBiology
10 months ago
info
▴ 10
0
votes
1
reply
533
views
DESeq2, Timecourse using fitted splines
timecoursedata
RNASeqData
TimeCourse
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
georgii.vdovin
• 0
1
vote
1
reply
471
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Sara
• 0
2
votes
1
reply
720
views
Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
oligoData
DataImport
oligo
RNASeqData
convert
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
rodj5201
• 0
0
votes
1
reply
587
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Abhishek Singh
▴ 20
3
votes
3
replies
986
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
10 months ago
amnahsiddiqa
▴ 10
50 results • Page
1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
jane
• 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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