Showing : RNA • reset
0
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3
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491
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
3 months ago gallantk5 • 0
0
votes
5
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949
views
Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 8 months ago by 67k • written 8 months ago by • 0
0
votes
1
reply
525
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 9 months ago by 42k • written 9 months ago by • 0
0
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2
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1.4k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 19 months ago by ★ 2.1k • written 19 months ago by • 0
3
votes
6
replies
2.5k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
23 months ago Sara • 0
0
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0
replies
663
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.0 years ago rridley3 • 0
1
vote
1
reply
900
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 2.1 years ago by ★ 4.5k • written 2.1 years ago by ▴ 30
0
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0
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913
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
2.2 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
2
replies
988
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.2 years ago sreekalasn • 0
2
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1
reply
1.2k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 2.4 years ago by 51k • written 2.4 years ago by • 0
1
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2
replies
2.0k
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Is it necessary to standardize Combat in R?
RNA Combat sva R
2.4 years ago takemoto • 0
1
vote
1
reply
928
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.6 years ago by ▴ 100 • written 2.6 years ago by ▴ 10
0
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1
reply
1.0k
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.8 years ago by ★ 4.5k • written 2.8 years ago by • 0
0
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0
replies
765
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Cross-cultivar RNA-seq analysis
RNA Normalization
3.5 years ago nancy • 0
0
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4
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1.7k
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
3.5 years ago Nirad ▴ 10
0
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3
replies
2.5k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 3.9 years ago by 51k • written 3.9 years ago by ▴ 10
4
votes
3
replies
2.8k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 20
2
votes
7
replies
1.4k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
1
vote
1
reply
946
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
6
replies
1.6k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
0
votes
0
replies
945
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
5.3 years ago jmaanaki • 0
1
vote
1
reply
1.6k
views
how to filter genes in significant module?
RNA WGCNA filter
5.3 years ago modarzi ▴ 10
0
votes
2
replies
993
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 10
2
votes
1
reply
919
views
DESeq2 statistic and design
deseq2 RNA
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 10
5
votes
5
replies
1.6k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 20
2
votes
3
replies
1.5k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 5.6 years ago by ★ 13k • written 5.6 years ago by ▴ 20
1
vote
0
replies
1.1k
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
6.0 years ago l.brown ▴ 10
0
votes
0
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1.1k
views
R code for finding wobble/redundant positions in an RNA string
r code rna wobble
6.7 years ago fawazfebin ▴ 60
0
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1
reply
1.1k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 7.2 years ago by 42k • written 7.2 years ago by ▴ 20
0
votes
1
reply
1.5k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 7.2 years ago by 42k • written 7.2 years ago by ▴ 20
1
vote
1
reply
1.7k
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 7.4 years ago by ▴ 420 • written 7.4 years ago by ▴ 30
5
votes
4
replies
1.4k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 7.5 years ago by • 0 • written 7.5 years ago by ▴ 40
3
votes
6
replies
2.1k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.5 years ago by 67k • written 7.5 years ago by ▴ 20
6
votes
5
replies
4.2k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.5 years ago by 51k • written 7.5 years ago by ▴ 20
0
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0
replies
1.7k
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
7.6 years ago Walter F. Baumann ▴ 10
3
votes
1
reply
1.8k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
0
votes
4
replies
5.2k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 8.7 years ago by 42k • written 8.7 years ago by • 0
0
votes
2
replies
1.4k
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
10.1 years ago aristotele_m ▴ 40
38 results • Page 1 of 1
Recent ...
Replies
Answer: Analysis of 2*4 factorial design by Gordon Smyth 51k
This is covered by Section 9.5 of the limma User's Guide. The analysis with a single-factor is much better. Your definition of A2 vs A1 …
Comment: Zero intra-block correlation in RRBS analysis using voomLmFit with block by Gordon Smyth 51k
It might be ok to estimate the intrablock correlation from the M-values. But then, if you do that, you may as well do the whole analysis in…
Answer: limma technical repeat correction by Gordon Smyth 51k
The technical samples should be averaged. Then use duplicateCorrelation() with block=PatientID.
Comment: New to mass spec data analysis by abhisek001 • 0
Thanks for your kind responses.
Comment: Duplicate row.names when building SummarizedExperiment with make_se in DEP by Anni • 0
I encountered the same problem. Problem seems to be "make_se()" function that does *not* use variable 'label' to bind colData to assay, but…
Votes
Differential expression analysis starting from TPM data
Answer: How to identify top most variable genes from log2 normalized data?
Answer: How to identify top most variable genes from log2 normalized data?
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Answer: clusterProfiler enrichGO on only T-cell related GO terms
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