Showing : Rna • reset
3
votes
6
replies
336
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
11 weeks ago • updated 10 weeks ago Sara • 0
0
votes
0
replies
98
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3 months ago rridley3 • 0
0
votes
1
reply
172
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
0
votes
0
replies
247
views
Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
5 months ago António Miguel de Jesus Domingues ▴ 490
0
votes
2
replies
291
views
Rsubread align --R session aborts
RNA Alignment Rsubread
6 months ago • updated 5 months ago sreekalasn • 0
2
votes
1
reply
298
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 7 months ago by 47k • written 7 months ago by • 0
1
vote
2
replies
482
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
8 months ago takemoto • 0
1
vote
1
reply
316
views
Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 11 months ago by ▴ 80 • written 11 months ago by ▴ 10
0
votes
1
reply
382
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 13 months ago by ★ 2.1k • written 13 months ago by • 0
0
votes
0
replies
310
views
Cross-cultivar RNA-seq analysis
RNA Normalization
21 months ago nancy • 0
0
votes
4
replies
690
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
22 months ago Nirad • 0
0
votes
3
replies
1.1k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 2.2 years ago by 47k • written 2.2 years ago by • 0
4
votes
3
replies
950
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 2.3 years ago by 62k • written 2.3 years ago by ▴ 20
2
votes
7
replies
645
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 2.7 years ago by 62k • written 2.7 years ago by • 0
1
vote
1
reply
384
views
How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 2.8 years ago by 39k • written 2.8 years ago by • 0
0
votes
6
replies
578
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 2.9 years ago by 39k • written 2.9 years ago by • 0
0
votes
0
replies
508
views
Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
3.6 years ago jmaanaki • 0
1
vote
1
reply
736
views
how to filter genes in significant module?
RNA WGCNA filter
3.6 years ago modarzi ▴ 10
0
votes
2
replies
550
views
DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 3.8 years ago by 39k • written 3.8 years ago by ▴ 10
2
votes
1
reply
458
views
DESeq2 statistic and design
deseq2 RNA
updated 3.8 years ago by 39k • written 3.8 years ago by ▴ 10
5
votes
5
replies
824
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 20
2
votes
3
replies
703
views
Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 3.9 years ago by 13k • written 3.9 years ago by ▴ 20
1
vote
0
replies
597
views
Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
4.3 years ago l.brown ▴ 10
0
votes
0
replies
578
views
R code for finding wobble/redundant positions in an RNA string
r code rna wobble
5.0 years ago fawazfebin ▴ 50
0
votes
1
reply
657
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 5.5 years ago by 39k • written 5.5 years ago by ▴ 20
0
votes
1
reply
1.1k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 5.5 years ago by 39k • written 5.5 years ago by ▴ 20
1
vote
1
reply
850
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 5.7 years ago by ▴ 400 • written 5.7 years ago by ▴ 30
5
votes
4
replies
928
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 5.7 years ago by • 0 • written 5.7 years ago by ▴ 40
3
votes
6
replies
1.4k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 5.8 years ago by 62k • written 5.8 years ago by ▴ 20
6
votes
5
replies
2.8k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 5.8 years ago by 47k • written 5.8 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
5.9 years ago Walter F. Baumann ▴ 10
3
votes
1
reply
1.3k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
0
votes
4
replies
4.4k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 6.9 years ago by 39k • written 6.9 years ago by • 0
0
votes
2
replies
973
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
8.3 years ago aristotele_m ▴ 30
34 results • Page 1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am recuctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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