Questions tagged [bioconductor]
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
9
questions
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votes
1
answer
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Extracting expression data from GSE dataset downloaded from GEO
I have downloaded GSE16146 dataset from GEO using GEOquery R package.
I would like to extract "Data table" from downloaded GSE16146.
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19
votes
2
answers
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Understanding DESeq2 design, contrast and results
I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 ...
- 3,090
16
votes
3
answers
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R package development: How does one automatically install Bioconductor packages upon package installation?
I have an R package on github which uses multiple Bioconductor dependencies, 'myPackage'
If I include CRAN packages in the DESCRIPTION via Depends:, the packages ...
- 1,681
6
votes
2
answers
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Transcript Coordinate Ranges to Genomic Coordinates
I have 2 GFF3 files:
Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space.
Features using chromosome IDs as the landmarks. i.e. "exon" ...
4
votes
1
answer
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Hierarchical models with limma?
I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
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4
votes
1
answer
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How should I address batch effects in my experiment?
Let's say I have an RNA-Seq experiment, where I'm interested in the significantly differentiated genes between pre-treatment and post-treatment conditions. "rep" == biological replicate.
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3
votes
1
answer
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alpha diversity wilcox.test
I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column.
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2
votes
1
answer
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GEO Methylation dataset "GSE73303" shows 0 features
I'm working for a project using GEO, in order to analyze some gene expression data. The SuperSeries I am referring to is GSE73304, but I found some problems working on the SubSeries GSE73303.
I ...
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votes
3
answers
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isSpike function in SingleCellExperiment package is deprecated?
I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use isSpike function to filter out ERCC (control) and MT (mitochondrial RNA) reads, ...
