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
written 11 months ago by • 0
0
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3
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902
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
15 months ago gallantk5 • 0
0
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5
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1.7k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 20 months ago by 68k • written 20 months ago by • 0
0
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1
reply
820
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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2
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2.3k
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Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 2.6 years ago by ★ 2.1k • written 2.6 years ago by • 0
3
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6
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3.4k
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
2.9 years ago Sara • 0
0
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0
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924
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.0 years ago rridley3 • 0
1
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1
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1.2k
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 30
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1.1k
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
3.2 years ago António Miguel de Jesus Domingues ▴ 510
0
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2
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1.3k
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Rsubread align --R session aborts
RNA Alignment Rsubread
3.2 years ago sreekalasn • 0
2
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1
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1.7k
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Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
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2
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2.5k
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Is it necessary to standardize Combat in R?
RNA Combat sva R
3.4 years ago takemoto • 0
1
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1
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1.2k
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by ▴ 10
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1
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1.3k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by • 0
0
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0
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933
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Cross-cultivar RNA-seq analysis
RNA Normalization
4.5 years ago nancy • 0
0
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4
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2.1k
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Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
4.5 years ago Nirad ▴ 10
0
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3
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3.1k
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Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 10
4
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3
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3.5k
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How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 20
2
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7
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1.8k
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Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
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1
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1.2k
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How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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6
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2.1k
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Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
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0
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1.2k
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
6.3 years ago jmaanaki • 0
1
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1
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2.0k
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how to filter genes in significant module?
RNA WGCNA filter
6.3 years ago modarzi ▴ 10
0
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2
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1.2k
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DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
2
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1
reply
1.1k
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DESeq2 statistic and design
deseq2 RNA
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
5
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5
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2.1k
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 20
2
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3
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2.2k
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Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 20
1
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0
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1.3k
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Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
7.0 years ago l.brown ▴ 10
0
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0
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1.4k
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R code for finding wobble/redundant positions in an RNA string
r code rna wobble
7.7 years ago fawazfebin ▴ 60
0
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1
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1.4k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
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1
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1.7k
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RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
1
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1
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2.4k
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Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 8.4 years ago by ▴ 420 • written 8.4 years ago by ▴ 30
5
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4
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1.7k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 8.5 years ago by • 0 • written 8.5 years ago by ▴ 40
3
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6
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2.5k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 8.5 years ago by 68k • written 8.5 years ago by ▴ 20
6
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5
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4.9k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 20
0
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0
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1.8k
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Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
8.6 years ago Walter F. Baumann ▴ 10
3
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1
reply
2.0k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
0
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4
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5.6k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
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2
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1.6k
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Normalizzation indipentent data from RNAAeq experiment
rna normalization
11.1 years ago aristotele_m ▴ 40
39 results • Page 1 of 1
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Answer: Issue with Soft-Thresholding in WGCNA by misty.chickadee.vckc • 0
Hi Maria, your detailed explanation is super helpful! The NA power estimate in WGCNA can be tricky. I've sometimes seen that when the data …
Comment: Interpretation of output of AffyRNAdeg and hist commands by debasainalsa • 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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