Showing : Rna • reset
5
votes
4
replies
1.3k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
9.5 years ago aristotele_m ▴ 40
3
votes
6
replies
1.9k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
17 months ago Sara • 0
6
votes
5
replies
3.8k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.0 years ago by 50k • written 7.0 years ago by ▴ 20
3
votes
6
replies
1.9k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 20
1
vote
1
reply
1.3k
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by ▴ 30
0
votes
1
reply
1.4k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 20
0
votes
1
reply
977
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 20
0
votes
2
replies
1.0k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 12 months ago by ★ 2.0k • written 12 months ago by • 0
0
votes
4
replies
5.0k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 8.1 years ago by 41k • written 8.1 years ago by • 0
3
votes
1
reply
1.6k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
2
votes
7
replies
1.2k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
4
votes
3
replies
2.2k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 20
0
votes
3
replies
2.2k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 3.4 years ago by 50k • written 3.4 years ago by ▴ 10
2
votes
1
reply
998
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 22 months ago by 50k • written 22 months ago by • 0
0
votes
1
reply
257
views
Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
0
votes
4
replies
1.3k
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
3.0 years ago Nirad ▴ 10
1
vote
1
reply
772
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
23 months ago takemoto • 0
0
votes
1
reply
856
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
0
votes
5
replies
431
views
Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
3
replies
1.1k
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 5.1 years ago by ★ 13k • written 5.1 years ago by ▴ 20
5
votes
5
replies
1.4k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
2
votes
1
reply
811
views
DESeq2 statistic and design
deseq2 RNA
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 10
0
votes
2
replies
873
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 10
0
votes
6
replies
1.2k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
1
vote
1
reply
773
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
1
vote
0
replies
927
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
5.5 years ago l.brown ▴ 10
0
votes
0
replies
927
views
R code for finding wobble/redundant positions in an RNA string
r code rna wobble
6.2 years ago fawazfebin ▴ 60
0
votes
0
replies
515
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
18 months ago rridley3 • 0
0
votes
0
replies
1.5k
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
7.1 years ago Walter F. Baumann ▴ 10
1
vote
1
reply
688
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 19 months ago by ★ 4.0k • written 19 months ago by ▴ 30
1
vote
1
reply
1.3k
views
how to filter genes in significant module?
RNA WGCNA filter
4.8 years ago modarzi ▴ 10
0
votes
0
replies
800
views
Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
4.8 years ago jmaanaki • 0
0
votes
2
replies
819
views
Rsubread align --R session aborts
RNA Alignment Rsubread
20 months ago sreekalasn • 0
0
votes
0
replies
756
views
Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
20 months ago António Miguel de Jesus Domingues ▴ 490
0
votes
0
replies
581
views
Cross-cultivar RNA-seq analysis
RNA Normalization
3.0 years ago nancy • 0
37 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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