Showing : rna • reset
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA RNASeqPower DEGseq
updated 18 days ago by 52k • written 20 days ago by • 0
0
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3
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543
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
4 months ago gallantk5 • 0
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5
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1.0k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 9 months ago by 67k • written 10 months ago by • 0
0
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1
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572
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
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2
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1.6k
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Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 20 months ago by ★ 2.1k • written 20 months ago by • 0
3
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6
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2.6k
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
2.1 years ago • updated 2.0 years ago Sara • 0
0
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0
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678
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.1 years ago rridley3 • 0
1
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1
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929
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by ▴ 30
0
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0
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937
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
2.3 years ago António Miguel de Jesus Domingues ▴ 510
0
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2
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1.0k
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Rsubread align --R session aborts
RNA Alignment Rsubread
2.3 years ago sreekalasn • 0
2
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1
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1.3k
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Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
1
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2
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2.1k
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Is it necessary to standardize Combat in R?
RNA Combat sva R
2.6 years ago • updated 2.5 years ago takemoto • 0
1
vote
1
reply
950
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.8 years ago by ▴ 100 • written 2.8 years ago by ▴ 10
0
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1
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1.1k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.9 years ago by ★ 4.6k • written 2.9 years ago by • 0
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784
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Cross-cultivar RNA-seq analysis
RNA Normalization
3.6 years ago nancy • 0
0
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4
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1.7k
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Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
3.7 years ago Nirad ▴ 10
0
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3
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2.6k
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Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4.1 years ago by 52k • written 4.1 years ago by ▴ 10
4
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3
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2.9k
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How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 20
2
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7
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1.5k
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Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
1
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1
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989
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How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
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6
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1.6k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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0
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997
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
5.4 years ago jmaanaki • 0
1
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1
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1.6k
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how to filter genes in significant module?
RNA WGCNA filter
5.4 years ago modarzi ▴ 10
0
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2
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1.0k
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DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
2
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1
reply
949
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DESeq2 statistic and design
deseq2 RNA
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
5
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5
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1.7k
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 20
2
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3
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1.6k
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Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 20
1
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0
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1.1k
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Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
6.1 years ago l.brown ▴ 10
0
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0
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1.1k
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R code for finding wobble/redundant positions in an RNA string
r code rna wobble
6.8 years ago fawazfebin ▴ 60
0
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1
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1.2k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
0
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1
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1.5k
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RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
1
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1
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1.8k
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Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 7.5 years ago by ▴ 420 • written 7.5 years ago by ▴ 30
5
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4
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1.5k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 7.6 years ago by • 0 • written 7.6 years ago by ▴ 40
3
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6
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2.1k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.6 years ago by 67k • written 7.6 years ago by ▴ 20
6
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5
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4.3k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 20
0
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0
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1.7k
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Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
7.7 years ago Walter F. Baumann ▴ 10
3
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1
reply
1.8k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
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4
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5.2k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
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2
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1.4k
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Normalizzation indipentent data from RNAAeq experiment
rna normalization
10.2 years ago aristotele_m ▴ 40
39 results • Page 1 of 1
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Comment: Running multiple KNN queries in parallel by SamGG ▴ 360
Thank you for your detailed answer, I appreciate it and your work.
Answer: Running multiple KNN queries in parallel by Aaron Lun ★ 28k
That is correct - you can't pass the prebuilt objects to different processes. Maybe `MulticoreParam()` might work on POSIX systems but I'm …
Answer: RSubread output significantly different from bash Subread output by Gordon Smyth 52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square by Michael Love 43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Votes
Answer: Running multiple KNN queries in parallel
Answer: Running multiple KNN queries in parallel
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
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