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 5 months ago by • 0
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3
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729
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
9 months ago gallantk5 • 0
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5
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 14 months ago by 68k • written 14 months ago by • 0
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1
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712
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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1.9k
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Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 2.1 years ago by ★ 2.1k • written 2.1 years ago by • 0
3
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6
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
2.4 years ago Sara • 0
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785
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.5 years ago rridley3 • 0
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 2.6 years ago by ★ 4.8k • written 2.6 years ago by ▴ 30
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
2.7 years ago António Miguel de Jesus Domingues ▴ 510
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Rsubread align --R session aborts
RNA Alignment Rsubread
2.7 years ago sreekalasn • 0
2
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1.5k
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Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
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Is it necessary to standardize Combat in R?
RNA Combat sva R
2.9 years ago takemoto • 0
1
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1.1k
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.1 years ago by ▴ 100 • written 3.1 years ago by ▴ 10
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.3 years ago by ★ 4.8k • written 3.3 years ago by • 0
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Cross-cultivar RNA-seq analysis
RNA Normalization
4.0 years ago nancy • 0
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1.9k
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Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
4.0 years ago Nirad ▴ 10
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3
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2.9k
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Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4.4 years ago by 52k • written 4.4 years ago by ▴ 10
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How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 20
2
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7
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Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
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1.1k
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How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
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6
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1.9k
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Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
5.8 years ago jmaanaki • 0
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1.8k
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how to filter genes in significant module?
RNA WGCNA filter
5.8 years ago modarzi ▴ 10
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1.1k
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DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
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1.0k
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DESeq2 statistic and design
deseq2 RNA
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
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5
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1.9k
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 20
2
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3
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2.0k
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Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 6.1 years ago by ★ 13k • written 6.1 years ago by ▴ 20
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Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
6.5 years ago l.brown ▴ 10
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1.2k
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R code for finding wobble/redundant positions in an RNA string
r code rna wobble
7.2 years ago fawazfebin ▴ 60
0
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1.3k
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Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
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1.6k
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RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
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2.2k
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Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 7.9 years ago by ▴ 420 • written 7.9 years ago by ▴ 30
5
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4
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1.6k
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Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 8.0 years ago by • 0 • written 8.0 years ago by ▴ 40
3
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6
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2.3k
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Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 20
6
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5
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4.6k
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Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.0 years ago by 52k • written 8.0 years ago by ▴ 20
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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
8.1 years ago Walter F. Baumann ▴ 10
3
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1
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1.9k
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Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
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4
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5.4k
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RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
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1.5k
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Normalizzation indipentent data from RNAAeq experiment
rna normalization
10.6 years ago aristotele_m ▴ 40
39 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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