Showing : RNASeq • reset
0
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3
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93
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 hours ago by ★ 4.1k • written 1 day ago by • 0
8
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6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 200 • written 6.7 years ago by ▴ 80
0
votes
1
reply
131
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 0
0
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2
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150
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 10 days ago by • 0
0
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2
replies
196
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
13 days ago • updated 10 days ago catv • 0
3
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1
reply
160
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Log-cpm values from limma
limma edgeR RNASeq
updated 13 days ago by 50k • written 14 days ago by • 0
0
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1
reply
106
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 14 days ago by 41k • written 14 days ago by • 0
0
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1
reply
133
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 22 days ago by ★ 4.1k • written 24 days ago by • 0
0
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2
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226
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
2
votes
2
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257
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
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2
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259
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
1
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4
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302
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DESeq2 Replicates
DESeq2 RNASeq
8 weeks ago kcarey • 0
1
vote
3
replies
356
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 10
0
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4
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296
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
0
votes
2
replies
290
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
3
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5
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615
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
2
votes
1
reply
259
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
3
votes
6
replies
525
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
10 weeks ago boczniak767 ▴ 720
0
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0
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219
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 weeks ago Abril • 0
2
votes
2
replies
406
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
12 weeks ago jackafiore • 0
1
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2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
392
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Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
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3
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332
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
569
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
231
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 200 • written 3 months ago by • 0
2
votes
4
replies
579
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
586
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
3
votes
1
reply
291
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
0
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3
replies
476
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
votes
1
reply
266
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
votes
3
replies
1.2k
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 ★ 1.3k • written 4 months ago by • 0
1
vote
2
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456
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
2
replies
438
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
797
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
3
replies
453
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
1
reply
373
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
2
votes
3
replies
467
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
replies
403
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
602
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
434
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 5 months ago by 41k • written 6 months ago by • 0
0
votes
2
replies
531
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 6 months ago by ▴ 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 • 0 • written 6.5 years ago by ▴ 60
1
vote
4
replies
623
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
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0
replies
353
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
4
votes
2
replies
622
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
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6
replies
841
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
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0
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335
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
0
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2
replies
636
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
0
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0
replies
277
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
0
votes
0
replies
335
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
50 results • Page 1 of 1
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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