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Showing :
RNASeqData
•
reset
22
votes
15
replies
7.6k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 6 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
5
votes
6
replies
596
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
3 months ago
Shaimaa Gamal
• 0
3
votes
5
replies
664
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 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
3
votes
2
replies
687
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
CDSPARKS
▴ 10
3
votes
3
replies
970
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
3
votes
4
replies
556
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 0
2
votes
1
reply
715
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
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
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 29 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
amnahsiddiqa
▴ 10
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
2
votes
4
replies
721
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
7 months ago
Shihui
• 0
2
votes
2
replies
436
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
1
vote
1
reply
611
views
DESEQ2 differential expression for subsets of data?
RNASeqData
DESeq2
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
amnahsiddiqa
▴ 10
1
vote
1
reply
401
views
Deseq contrast question
RNASeqData
DESeq2
updated 11 months ago by
Michael Love
42k • written 11 months ago by
Hannah
▴ 10
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
2
replies
697
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
1
vote
1
reply
352
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
kaurprab
• 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
1
vote
9
replies
906
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Matteo
• 0
1
vote
3
replies
357
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
3 months ago
island
• 0
1
vote
1
reply
415
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
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
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
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
7
replies
873
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
1
vote
2
replies
539
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
1
vote
1
reply
473
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
1
reply
121
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Leyre
• 0
0
votes
2
replies
743
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
6 months ago
RHEA
• 0
0
votes
1
reply
580
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
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
0
votes
0
replies
25
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
17 hours ago
Shaimaa Gamal
• 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
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
0
votes
1
reply
404
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
3
replies
731
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
5 months ago
Oenone
• 0
0
votes
2
replies
372
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
5 months ago
Luca
• 0
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
0
replies
340
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
10 months ago
sonal
• 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
0
votes
0
replies
402
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
10 months ago
amnahsiddiqa
▴ 10
0
votes
6
replies
805
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
0
votes
1
reply
681
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
1
reply
365
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
0
votes
0
replies
242
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
3 months ago
Abril
• 0
0
votes
1
reply
510
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
0
replies
559
views
News:
Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor
Network
RNASeqData
SystemsBiology
10 months ago
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
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
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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