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Showing :
RNAseq
•
reset
2
votes
2
replies
138
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 days ago • updated 4 days ago
Sabiha
▴ 20
0
votes
2
replies
120
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 days ago • updated 4 days ago
kcarey
• 0
1
vote
4
replies
206
views
DESeq2 Replicates
DESeq2
RNASeq
12 days ago
kcarey
• 0
1
vote
3
replies
234
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 14 days ago by
swbarnes2
★ 1.3k • written 17 days ago by
sap275
▴ 10
0
votes
4
replies
191
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
20 days ago • updated 18 days ago
mperalc
• 0
0
votes
2
replies
172
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 21 days ago by
Gordon Smyth
50k • written 21 days ago by
ryann
• 0
3
votes
5
replies
485
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 14 days ago by
Michael Love
41k • written 24 days ago by
sap275
▴ 10
2
votes
1
reply
179
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 21 days ago by
Michael Love
41k • written 22 days ago by
sap275
▴ 10
3
votes
6
replies
388
views
Average biological replicates in RNA-seq
Mfuzz
RNASeq
28 days ago • updated 26 days ago
boczniak767
▴ 720
0
votes
0
replies
135
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
4 weeks ago
Abril
• 0
2
votes
2
replies
259
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
5 weeks ago
jackafiore
• 0
1
vote
2
replies
965
views
How to combine a bulk and pseudobulk dataset?
DESeq2
limma
RNASeq
RNASeqData
written 10 months ago by
informatician
• 0
0
votes
4
replies
289
views
Ballgown error in scan for c.tab files
ballgown
RNASeq
6 weeks ago
candacenewcome
• 0
1
vote
3
replies
263
views
DESeq2 analysis on time-series RNA experiment
RNASeqData
DESeq2
RNASeq
7 weeks ago • updated 6 weeks ago
island
• 0
1
vote
3
replies
461
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 7 weeks ago by
georgii.vdovin
• 0
0
votes
1
reply
162
views
Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 7 weeks ago by
Ram
▴ 190 • written 7 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
4
replies
426
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
8 weeks ago
Sabiha
▴ 20
4
votes
6
replies
467
views
filtering lowly expressed reads
RNASeq
limma
DifferentialExpression
Preprocessing
updated 5 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Shaimaa Gamal
• 0
3
votes
1
reply
200
views
Dataset imbalance
RNASeq
DifferentialExpression
RnaSeqSampleSizeData
RnaSeqSampleSize
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Shaimaa Gamal
• 0
0
votes
3
replies
326
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 9 weeks ago by
Fayrouz
• 0
0
votes
1
reply
201
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
9 weeks ago
WS
• 0
2
votes
3
replies
915
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 12 weeks ago by
swbarnes2
★ 1.3k • written 3 months ago by
Bo
• 0
1
vote
2
replies
355
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
12 weeks ago
Sabiha
▴ 20
1
vote
2
replies
362
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
3 months ago
drewhaydensteele
• 0
7
votes
2
replies
575
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
0
votes
3
replies
385
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
3 months ago
Karthik
• 0
1
vote
1
reply
325
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 3 months ago by
Michael Love
41k • written 3 months ago by
pl23
• 0
2
votes
3
replies
378
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
3 months ago
Karthik
• 0
2
votes
2
replies
340
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
3 months ago
Manthos
• 0
2
votes
4
replies
534
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom
RNASeq
limma
4 months ago
Tyler Sagendorf
▴ 10
0
votes
1
reply
382
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 4 months ago by
Michael Love
41k • written 5 months ago by
Sean
• 0
0
votes
2
replies
451
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 4 months ago by
Leonardo Collado Torres
★ 1.0k • written 4 months ago by
tangming2005
▴ 190
0
votes
9
replies
2.4k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 4 months ago by
blowfish
• 0 • written 6.4 years ago by
bharata1803
▴ 60
1
vote
4
replies
542
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
4 months ago
Wending
• 0
0
votes
0
replies
301
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
4 months ago
mch
• 0
4
votes
2
replies
501
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
alvaroperona1
▴ 10
0
votes
6
replies
693
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
4 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
278
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
5 months ago
Sara
• 0
0
votes
2
replies
578
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
5 months ago • updated 4 months ago
Karthik
• 0
0
votes
0
replies
228
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
0
votes
0
replies
280
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
5 months ago
Xinqi
• 0
0
votes
0
replies
271
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
5 months ago
Sara
• 0
1
vote
1
reply
333
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
fuqichen1
• 0
1
vote
7
replies
727
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 3 months ago by
Gordon Smyth
50k • written 5 months ago by
Gimena
• 0
0
votes
2
replies
367
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 5 months ago by
swbarnes2
★ 1.3k • written 5 months ago by
Jules
• 0
0
votes
1
reply
358
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 5 months ago by
Basti
▴ 750 • written 5 months ago by
Luke
• 0
3
votes
5
replies
686
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 6 months ago by
ATpoint
★ 3.9k • written 6 months ago by
Shashank
• 0
1
vote
1
reply
399
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 6 months ago by
ATpoint
★ 3.9k • written 6 months ago by
jg0428
• 0
0
votes
1
reply
513
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
Adam
• 0
1
vote
6
replies
765
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 7 months ago by
ATpoint
★ 3.9k • written 7 months ago by
Debebe
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Comment: BioC2024 abstract submission is open!
by
howell
• 0
What are the conditions for approval of people in difficult circumstances? I want this scholarship
Comment: European Bioconductor Conference 2023 planning
by
william
• 0
[@MariaDoyle][1] Without a doubt. In that position, I will be included in the discussion. [1]: https://support.bioconductor.org/u/239…
Comment: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
Georg
• 0
Thank you for the detailed response. The code worked right away. I appreciate the quick response.
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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