17 votes
Accepted

Why Bioconductor?

Benefits of central repository for Community Having a central repository for packages is very useful. For couple of reasons: It makes very easy to resolve dependencies. Installing all the ...
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  • 5,287
16 votes

R package development: How does one automatically install Bioconductor packages upon package installation?

As suggested, here’s an example showing the relevant lines from a DESCRIPTION file from a CRAN/GitHub hosted project that has Bioconductor dependencies (truncated): ...
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14 votes

Understanding DESeq2 design, contrast and results

The simplest manner is to not use a wald test, but rather an LRT with a reduced model lacking the factor of interest: ...
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  • 19.3k
12 votes
Accepted

How can I extract normalized read count values from DESeq2 results?

The normalized counts themselves can be accessed with counts(dds, normalized=T). Now as to what the baseMean actually means, that will depend upon whether an "...
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  • 19.3k
9 votes

Why Bioconductor?

Here is a list of the advantages of having Bioconductor for the bioinformatic community: Outreach: You have a repository for the field, in that language. Some packages related to bioinformatics (in ...
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  • 4,622
9 votes

What are the ways to keep track of branches in the analysis?

Save the different scripts with git (seems overkill) Whoa. I did an actual double take when reading this:1 it’s the opposite of overkill. Version controlling your scripts (using Git or something ...
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9 votes
Accepted

R package development: How does one automatically install Bioconductor packages upon package installation?

There's a trick to this where one needs to add biocViews: to the package Description. That's the only solution I've ever seen to allowing automatic installation of ...
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  • 19.3k
8 votes

Extracting expression data from GSE dataset downloaded from GEO

According to the manual, all you need to do is: library('GEOquery') gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE) As explanation, ...
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  • 2,614
8 votes

Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids

You need to specify the number without the version. Instead of "ENSMUST00000178862.1" just "ENSMUST00000178862": You can do this with one more line: ...
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  • 4,622
8 votes
Accepted

Understanding DESeq2 design, contrast and results

It seems that the "combining factors" trick described in part 3.3 of DESeq2 current "vignette" (as of may 2017) under the title "Interaction" is a way to access to the desired contrasts. It seems ...
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  • 2,920
8 votes
Accepted

How can I colour boxes in Gviz AnnotationTrack in R?

Did you try the fill argument? Something like this: ...
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  • 3,521
7 votes
Accepted

Are fgsea and Broad Institute GSEA equivalent?

According to the FGSEA preprint: We ran reference GSEA with default parameters. The permutation number was set to 1000, which means that for each input gene set 1000 independent samples were ...
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  • 2,099
7 votes
Accepted

How to identify gene expression signatures from gene expression data?

There is no golden/standard way to define a gene signature but they are completely different from a gene set enrichment analysis (GSEA). I will start with how to obtain a gene signature: Usually this ...
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  • 4,622
7 votes
Accepted

How to transform a DNAStringSet from the Bioconductor package Biostrings to a data frame?

According to the documentation (?Biostrings::DNAStringSet): width(x): A vector of non-negative integers containing the number ...
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6 votes

How can I extract normalized read count values from DESeq2 results?

It depends what you mean by “normalised”. As Devon said, the normalized = TRUE argument to the count function gives you ...
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6 votes
Accepted

Get RefSeq accession numbers with versions

I don't believe this is possible using biomaRt, nor using AnnotationHub. I have two suggestions, neither of them very ...
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  • 646
6 votes

Melt p-values for CpG sites mapping to the same gene

Methylation levels have high local correlation, so Fisher's method would be problematic. Having said that, you have no reason to use Fisher's method after a paired t-test. A paired t-test will give ...
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  • 19.3k
6 votes

Ensembl id to GeneSymbol with biomart

It looks like you were using an old annotation. The problematic IDs you posted existed in the GRCh37 annotations, but don't in the most recent GRCh38 annotation. For that reason they were excluded. ...
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  • 19.3k
6 votes
Accepted

Is there an efficient way to check an input BAM in R?

You won’t know whether it’s a valid BAM file until you attempt reading it in full; even Devon’s method (which I recommend) only does a superficial check — i.e. it checks whether (parts of) the BAM ...
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6 votes
Accepted

How to subset a GRanges via an argument passed into a function?

subsetter = function(gr, cname) { return(mcols(gr)[[cname]]) } You can then use things like subsetter(gr, "GC") and ...
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  • 19.3k
6 votes
Accepted

Error in as.vector(x) : no method for coercing this S4 class to a vector

You can't cbind a bunch of obscure object types. If you want merged count tables you should do this: mdat <- do.call(cbind,lapply(dat,assay)) Where row.names ...
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  • 1,468
5 votes
Accepted

What are the ways to keep track of branches in the analysis?

The main purpose of git is to version code, which usually means sequential improvement of the codebase. While it is possible to use branches for multiple variants of the software, permanent branches ...
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5 votes
Accepted

Running differential expression analyses on count matrices with many zeroes

I don't think that the issue is the low counts, but rather the number of features without any real variance (the black dots at the bottom). So what the heck is the dispersion plot and why does one ...
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  • 19.3k
5 votes
Accepted

Normalizing microarray data for clustering heat map

You see negative values with your function because you're setting the average of each row to 0 and its standard deviation to 1. In general, I would trust a standard normalization method (rma in this ...
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  • 19.3k
5 votes

Duplicate genes with RSEM counts: Which one to choose?

There is no one-to-one mapping of gene ids from one database to the other. Ensembl (who maintain Ensembl ENSG IDs), ncbi (who maintain EntrezGene IDs and RefSeq transcript ids) and HUGO (who maintain ...
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  • 3,201
5 votes
Accepted

Duplicate genes with RSEM counts: Which one to choose?

Let's look into this a bit more deeply. For instance: HUGO: SOGA3 Ensembl 1: ENSG00000214338 Ensembl 2: ENSG00000255330 The Ensembl pages (linked above) for both ENSG00000214338 and ENSG00000255330 ...
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  • 7,957
5 votes

SNP located within a promoter region (pig)

As far as I'm aware, Illumina provide CSV annotation files for all their sequencing chips, which can be used when they can't be found in Bioconductor. You can find annotation information for the ...
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  • 11.5k
5 votes
Accepted

Is there a Python/R package with the ability to convert an alignment and reference into a CIGAR?

Your request is easy to implement. I wouldn't use any libraries in this case. As you haven't showed your implementation, I will provide one: ...
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  • 5,645
5 votes

How to subset a GRanges via an argument passed into a function?

In such cases it is best to check the str of an object gr. Then we could see that meta data is just a dataframe inside S4 object: ...
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  • 1,052
5 votes
Accepted

Can I submit a R package to Bioconductor or CRAN if I have already published it a journal?

You can submit a package to a repo after the publication, but I would say that you really should do it before. Bioconductor accept only packages that are not published on CRAN, however, academic ...
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  • 5,287

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