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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911
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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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1.8k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 21 months ago by 68k • written 21 months ago by • 0
0
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1
reply
856
views
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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2.4k
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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
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.0 years ago Sara • 0
0
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0
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962
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.1 years ago rridley3 • 0
1
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1
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1.2k
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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 3.2 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
3.2 years ago António Miguel de Jesus Domingues ▴ 510
0
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2
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1.4k
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Rsubread align --R session aborts
RNA Alignment Rsubread
3.3 years ago • updated 3.2 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 3.4 years ago by 53k • written 3.4 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
3.5 years ago takemoto • 0
1
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1
reply
1.2k
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.7 years ago by ▴ 100 • written 3.7 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 3.8 years ago by ★ 5.0k • written 3.8 years ago by • 0
0
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0
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968
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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
4.6 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 5.0 years ago by 53k • written 5.0 years ago by ▴ 10
4
votes
3
replies
3.5k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 20
2
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7
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1.8k
views
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 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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6
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2.1k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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0
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1.2k
views
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
reply
2.0k
views
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 6.6 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 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
5
votes
5
replies
2.1k
views
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
views
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
views
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
views
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
reply
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
reply
1.7k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 20
1
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1
reply
2.5k
views
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 8.5 years ago by • 0 • written 8.5 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
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5
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5.0k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.6 years ago by 53k • written 8.6 years ago by ▴ 20
0
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0
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1.8k
views
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
votes
1
reply
2.0k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 9.1 years ago by ★ 29k • written 9.2 years ago by • 0
0
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4
replies
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
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
11.1 years ago aristotele_m ▴ 40
39 results • Page 1 of 1
Recent ...
Replies
Comment: VariantAnnotation does escape = within header string quotes by Daniel Cameron ▴ 40
I'm just stripping the entire line as a workaround using `meta(header(vcf))$DRAGENCommandLine = NULL`. Not ideal but at least subsequent pa…
Comment: Setting up a DESeq2 Design with Paired Data by Alexander • 0
Hi Kevin, Firstly, thank you so much for not only a very prompt response, but one that is incredibly insightful and helps me learn DESeq2 …
Comment: featureCounts -L: high unassigned:mapq fraction by eja.gssssssse.r.m • 0
If you re looking to enjoy a fun mobile experience, the 3 patti vegas game offers a seamless way to play classic card games on your phone. …
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Kevin Blighe ★ 4.0k
Hello Matthew, Thanks for the detailed description-this sounds like a classic challenge in sncRNA analysis, where piRNAs (and other tsRN…
Answer: VariantAnnotation does escape = within header string quotes by Kevin Blighe ★ 4.0k
Hi, Thanks for the minimal reproduction - this is very clear and confirms a bug in `VariantAnnotation::writeVcf()`. The issue is that th…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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