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RNASEQ
•
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0
votes
0
replies
4
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
17 minutes ago
kcarey
• 0
0
votes
1
reply
82
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
taur.vil
• 0
0
votes
2
replies
147
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 days ago • updated 2 days ago
catv
• 0
0
votes
1
reply
107
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
84
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
0
votes
1
reply
119
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 14 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Merav
• 0
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
4 weeks ago
kcarey
• 0
2
votes
2
replies
243
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 weeks ago
Sabiha
▴ 20
0
votes
2
replies
236
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 weeks ago
kcarey
• 0
1
vote
4
replies
290
views
DESeq2 Replicates
DESeq2
RNASeq
6 weeks ago
kcarey
• 0
1
vote
3
replies
338
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 7 weeks ago by
swbarnes2
★ 1.3k • written 7 weeks ago by
sap275
▴ 10
0
votes
4
replies
272
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
8 weeks ago • updated 7 weeks ago
mperalc
• 0
0
votes
2
replies
259
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
ryann
• 0
3
votes
5
replies
599
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 7 weeks ago by
Michael Love
41k • written 8 weeks ago by
sap275
▴ 10
2
votes
1
reply
243
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 8 weeks ago by
Michael Love
41k • written 8 weeks ago by
sap275
▴ 10
3
votes
6
replies
502
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
9 weeks ago
boczniak767
▴ 720
0
votes
0
replies
201
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
9 weeks ago
Abril
• 0
2
votes
2
replies
375
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
11 weeks ago • updated 10 weeks ago
jackafiore
• 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 11 months ago by
informatician
• 0
0
votes
4
replies
371
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
12 weeks ago • updated 11 weeks ago
candacenewcome
• 0
1
vote
3
replies
318
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
12 weeks ago
island
• 0
1
vote
3
replies
552
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 12 weeks ago by
georgii.vdovin
• 0
0
votes
1
reply
219
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 3 months ago by
Ram
▴ 190 • written 3 months ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
541
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
4
votes
6
replies
554
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 10 weeks ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
3
votes
1
reply
263
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Shaimaa Gamal
• 0
0
votes
3
replies
453
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 3 months ago by
Fayrouz
• 0
0
votes
1
reply
254
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
3 months ago
WS
• 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
1
vote
2
replies
430
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
1
vote
2
replies
418
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
4 months ago
drewhaydensteele
• 0
7
votes
2
replies
759
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
0
votes
3
replies
439
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago • updated 4 months ago
Karthik
• 0
1
vote
1
reply
366
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 4 months ago by
Michael Love
41k • written 5 months ago by
pl23
• 0
2
votes
3
replies
450
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
5 months ago • updated 4 months ago
Karthik
• 0
2
votes
2
replies
388
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
2
votes
4
replies
588
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
5 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
424
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 5 months ago by
Michael Love
41k • written 6 months ago by
Sean
• 0
0
votes
2
replies
519
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 5 months ago by
Leonardo Collado Torres
★ 1.0k • written 6 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 5 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
1
vote
4
replies
603
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
5 months ago
Wending
• 0
0
votes
0
replies
339
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
5 months ago
mch
• 0
4
votes
2
replies
589
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
806
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
325
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
6 months ago
Sara
• 0
0
votes
2
replies
623
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
6 months ago
Karthik
• 0
0
votes
0
replies
262
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
0
votes
0
replies
325
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
6 months ago
Xinqi
• 0
0
votes
0
replies
328
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
6 months ago
Sara
• 0
1
vote
1
reply
398
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
fuqichen1
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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