Showing : Rna • reset
0
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5
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649
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 4 months ago by 66k • written 4 months ago by • 0
0
votes
1
reply
353
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
0
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2
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1.2k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 15 months ago by ★ 2.1k • written 15 months ago by • 0
3
votes
6
replies
2.1k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
19 months ago Sara • 0
0
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0
replies
569
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
20 months ago rridley3 • 0
1
vote
1
reply
782
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 21 months ago by ★ 4.2k • written 21 months ago by ▴ 30
0
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0
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826
views
Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
22 months ago António Miguel de Jesus Domingues ▴ 510
0
votes
2
replies
878
views
Rsubread align --R session aborts
RNA Alignment Rsubread
23 months ago • updated 22 months ago sreekalasn • 0
2
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1
reply
1.1k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 2.1 years ago by 51k • written 2.1 years ago by • 0
1
vote
2
replies
1.7k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.1 years ago takemoto • 0
1
vote
1
reply
822
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.3 years ago by ▴ 90 • written 2.3 years ago by ▴ 10
0
votes
1
reply
915
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.5 years ago by ★ 4.2k • written 2.5 years ago by • 0
0
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0
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651
views
Cross-cultivar RNA-seq analysis
RNA Normalization
3.2 years ago nancy • 0
0
votes
4
replies
1.4k
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
3.2 years ago Nirad ▴ 10
0
votes
3
replies
2.3k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 3.6 years ago by 51k • written 3.6 years ago by ▴ 10
4
votes
3
replies
2.4k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 3.7 years ago by 66k • written 3.7 years ago by ▴ 20
2
votes
7
replies
1.3k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 4.1 years ago by 66k • written 4.1 years ago by • 0
1
vote
1
reply
833
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
0
votes
6
replies
1.4k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
0
votes
0
replies
845
views
Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
5.0 years ago jmaanaki • 0
1
vote
1
reply
1.4k
views
how to filter genes in significant module?
RNA WGCNA filter
5.0 years ago modarzi ▴ 10
0
votes
2
replies
917
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 5.2 years ago by 42k • written 5.2 years ago by ▴ 10
2
votes
1
reply
853
views
DESeq2 statistic and design
deseq2 RNA
updated 5.2 years ago by 42k • written 5.2 years ago by ▴ 10
5
votes
5
replies
1.5k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
2
votes
3
replies
1.2k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 5.3 years ago by ★ 13k • written 5.3 years ago by ▴ 20
1
vote
0
replies
976
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
5.7 years ago l.brown ▴ 10
0
votes
0
replies
989
views
R code for finding wobble/redundant positions in an RNA string
r code rna wobble
6.4 years ago fawazfebin ▴ 60
0
votes
1
reply
1.0k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 20
0
votes
1
reply
1.4k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 7.1 years ago by ▴ 420 • written 7.1 years ago by ▴ 30
5
votes
4
replies
1.3k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 7.1 years ago by • 0 • written 7.1 years ago by ▴ 40
3
votes
6
replies
2.0k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.2 years ago by 66k • written 7.2 years ago by ▴ 20
6
votes
5
replies
4.0k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.2 years ago by 51k • written 7.2 years ago by ▴ 20
0
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0
replies
1.5k
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
7.3 years ago Walter F. Baumann ▴ 10
3
votes
1
reply
1.7k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
4
replies
5.1k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 8.3 years ago by 42k • written 8.3 years ago by • 0
0
votes
2
replies
1.3k
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
9.7 years ago aristotele_m ▴ 40
37 results • Page 1 of 1
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Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types) by Michael Love 42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results by Michael Love 42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results by V_Vibes • 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results by V_Vibes • 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
Votes
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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