Showing : variancePartition • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 9 weeks ago by 53k • written 10 weeks ago by • 0
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
11 months ago GJ • 0
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2
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940
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 months ago by 53k • written 12 months ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 12 months ago by 68k • written 12 months ago by • 0
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 15 months ago by 53k • written 15 months ago by • 0
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978
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
20 months ago Le • 0
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2.4k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
2.0 years ago hayleyw • 0
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1.8k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.0 years ago by 53k • written 2.2 years ago by • 0
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
2.3 years ago hayleyw • 0
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5
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.7 years ago • updated 2.6 years ago Weiqian ▴ 10
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4
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1.3k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.8 years ago DH • 0
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5
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1.9k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
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882
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.3 years ago Jonathan • 0
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1.9k
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
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3
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1.9k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 4.5 years ago by 53k • written 4.5 years ago by ▴ 30
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1.2k
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
4.6 years ago Junghoon ▴ 10
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1.7k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
4.6 years ago Junghoon ▴ 10
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1.6k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
4.6 years ago • updated 4.5 years ago Junghoon ▴ 10
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dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 20
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 6.2 years ago by ▴ 170 • written 6.3 years ago by • 0
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 6.2 years ago by ▴ 170 • written 6.5 years ago by ▴ 50
23 results • Page 1 of 1
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Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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