18
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 ...
- 5,517
18
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):
...
- 4,845
16
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:
...
- 19.6k
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 "...
- 19.6k
10
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 ...
- 3,100
10
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 ...
- 4,693
10
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 ...
- 19.6k
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 ...
- 4,845
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, ...
- 2,676
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:
...
- 4,693
8
votes
Accepted
How can I colour boxes in Gviz AnnotationTrack in R?
Did you try the fill argument?
Something like this:
...
- 3,571
8
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 ...
- 2,725
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 ...
- 2,169
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 ...
- 4,693
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 ...
- 4,845
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 ...
- 646
6
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 ...
- 19.6k
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 ...
- 19.6k
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. ...
- 19.6k
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 ...
- 4,845
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 ...
- 19.6k
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 ...
- 1,573
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 ...
- 2,725
5
votes
Running differential expression analyses on count matrices with many zeroes
Remove low-count features in advance. This is standard for most tools including DESeq2 and edgeR (see section 2.6).
This will keep you from testing a lot of features that cannot be differentially ...
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 ...
- 19.6k
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 ...
- 3,301
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 ...
- 9,662
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 ...
- 13.8k
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:
...
- 6,485
Only top scored, non community-wiki answers of a minimum length are eligible