Showing : rnaseq • reset
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6
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2.3k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.1 years ago erika.maldonado-rosado • 0
0
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0
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738
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is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
2.1 years ago Sara • 0
0
votes
2
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1.1k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
2.1 years ago Karthik • 0
0
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0
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722
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.1 years ago Florian • 0
0
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0
replies
993
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
2.1 years ago Xinqi • 0
0
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0
replies
870
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
2.1 years ago Sara • 0
1
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1
reply
1.0k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
7
replies
1.8k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 23 months ago by 53k • written 2.1 years ago by • 0
0
votes
2
replies
853
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
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1
reply
1.1k
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
3
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5
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2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
1
vote
1
reply
914
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
1
reply
849
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
vote
6
replies
3.4k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
6
votes
7
replies
1.5k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
0
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1
reply
5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
2
votes
1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.3 years ago mohammedtoufiq91 ▴ 10
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2
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1.3k
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.3 years ago Matteo • 0
4
votes
2
replies
3.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
0
votes
3
replies
1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
3
votes
11
replies
4.8k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.5 years ago • updated 2.4 years ago Anna ▴ 20
2
votes
9
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7.0k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.7 years ago by ▴ 10
0
votes
1
reply
875
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Anova table edgeR limma
limma RNASeq edgeR
2.5 years ago KATHERINE CHUERE NUNES • 0
1
vote
2
replies
1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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3
replies
1.4k
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
1
vote
3
replies
1.6k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
votes
2
replies
2.5k
views
model matrix not full rank
DESeq2 RNASeq
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 2.5 years ago by 43k • written 2.6 years ago by • 0
2
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3
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857
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RNA seq with edgeR with several factors
RNAseq factors
2.6 years ago Nathalie ▴ 20
0
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3
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1.3k
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
8
votes
10
replies
17k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 6 months ago by ★ 5.0k • written 9.3 years ago by ▴ 20
0
votes
4
replies
1.7k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
1
vote
1
reply
716
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
3
votes
12
replies
2.9k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
0
votes
1
reply
754
views
Sample expression calculation in rna seq
Rnaseq
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
1
vote
1
reply
903
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
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0
replies
959
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.6 years ago Levi • 0
4
votes
8
replies
6.1k
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
updated 2.6 years ago by • 0 • written 4.5 years ago by • 0
1
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2
replies
1.0k
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.6 years ago by • 0
2
votes
4
replies
1.4k
views
limma with or without intercept gives different results
limma rnaseq
2.6 years ago Sydney • 0
1
vote
2
replies
1.8k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.6 years ago garbuzov • 0
0
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2
replies
1.2k
views
Compare and filter three BAM files
RNAseq 10X
2.7 years ago • updated 2.6 years ago wt215 • 0
0
votes
5
replies
1.6k
views
hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
5
votes
7
replies
1.7k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 22 months ago by 53k • written 2.7 years ago by • 0
0
votes
2
replies
1.6k
views
GO analysis in R vs website
GO RNASeq
2.7 years ago Nitro • 0
1
vote
4
replies
1.3k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.7 years ago DH • 0
1
vote
0
replies
1.2k
views
Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
2.7 years ago Jamie Walters ▴ 10
3
votes
2
replies
1.5k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.7 years ago chf • 0
1,409 results • Page 3 of 29
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I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
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Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
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As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
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The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
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