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RNASeqData
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0
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0
replies
41
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
1 day ago
Shaimaa Gamal
• 0
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
z_bahari
• 0
0
votes
1
reply
123
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
667
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
242
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
358
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
3 months ago
island
• 0
0
votes
2
replies
291
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus
RNASeqData
3 months ago
Diana
• 0
0
votes
1
reply
331
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
597
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
3 months ago
Shaimaa Gamal
• 0
1
vote
1
reply
416
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
373
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
5 months ago
Luca
• 0
0
votes
1
reply
360
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
468
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
5 months ago
drewhaydensteele
• 0
1
vote
1
reply
353
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
699
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
732
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
559
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
366
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 5 months ago by
Michael Love
42k • written 6 months ago by
Pez
▴ 10
2
votes
2
replies
437
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
5 months ago
Manthos
• 0
0
votes
1
reply
406
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
469
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
747
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
6 months ago
RHEA
• 0
2
votes
3
replies
851
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
444
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
875
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
418
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
724
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
688
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 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
682
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
534
views
RSubread DESeq2
RNASeqData
DifferentialExpression
DESeq2
8 months ago
Beyza
• 0
1
vote
1
reply
474
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
340
views
How to use erccdashboard with erccmix="Single" design
RNASeqData
erccdashboard
8 months ago
adi.rotem
• 0
0
votes
1
reply
511
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
531
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
949
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
807
views
Questionable limma results for differential expression on RNA-seq
RNASeqData
DifferentialExpression
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
gld-bioinf
• 0
1
vote
2
replies
540
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 9 months ago by
Michael Love
42k • written 10 months ago by
mohammad.hossein.banabazi
• 0
0
votes
0
replies
342
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
10 months ago
sonal
• 0
1
vote
9
replies
908
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
529
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
469
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
716
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
582
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
976
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: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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