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 12 months ago by • 0
0
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3
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946
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
16 months ago gallantk5 • 0
0
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5
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1.8k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 22 months ago by 68k • written 22 months ago by • 0
0
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1
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876
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 22 months ago by 43k • written 23 months ago by • 0
0
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2
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2.5k
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Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 2.7 years ago by ★ 2.1k • written 2.7 years ago by • 0
3
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6
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3.5k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.1 years ago • updated 3.0 years ago Sara • 0
0
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0
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987
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.1 years ago rridley3 • 0
1
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1
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1.3k
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by ▴ 30
0
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0
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1.2k
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
3.3 years ago António Miguel de Jesus Domingues ▴ 510
0
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2
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1.5k
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Rsubread align --R session aborts
RNA Alignment Rsubread
3.3 years ago sreekalasn • 0
2
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1
reply
1.7k
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Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
1
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2
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2.6k
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Is it necessary to standardize Combat in R?
RNA Combat sva R
3.6 years ago • updated 3.5 years ago takemoto • 0
1
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1
reply
1.2k
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.8 years ago by ▴ 100 • written 3.8 years ago by ▴ 10
0
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1
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1.4k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by • 0
0
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0
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980
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Cross-cultivar RNA-seq analysis
RNA Normalization
4.6 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
4.7 years ago Nirad ▴ 10
0
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3
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3.1k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 10
4
votes
3
replies
3.6k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 20
2
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7
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1.9k
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Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
1
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1
reply
1.2k
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How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 5.6 years ago by 43k • written 5.6 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 5.8 years ago by 43k • written 5.8 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
6.4 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
6.4 years ago modarzi ▴ 10
0
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2
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1.3k
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
2
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1
reply
1.1k
views
DESeq2 statistic and design
deseq2 RNA
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
5
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5
replies
2.1k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 6.7 years ago by ★ 29k • written 6.7 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 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 20
1
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0
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1.3k
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
7.1 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
7.8 years ago fawazfebin ▴ 60
0
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1
reply
1.4k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 20
0
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1
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1.7k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 20
1
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1
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2.5k
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Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 8.5 years ago by ▴ 420 • written 8.5 years ago by ▴ 30
5
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4
replies
1.8k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 8.6 years ago by • 0 • written 8.6 years ago by ▴ 40
3
votes
6
replies
2.5k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 20
6
votes
5
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5.0k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 20
0
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0
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1.9k
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
8.7 years ago Walter F. Baumann ▴ 10
3
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1
reply
2.1k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 9.2 years ago by ★ 29k • written 9.2 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 9.8 years ago by 43k • written 9.8 years ago by • 0
0
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2
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1.6k
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
11.2 years ago aristotele_m ▴ 40
39 results • Page 1 of 1
Recent ...
Replies
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.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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