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32 votes
Accepted

How to compute RPKM in R?

First off, Don’t use RPKMs. They are truly deprecated because they’re confusing once it comes to paired-end reads. If anything, use FPKMs, which are mathematically the same but use a more correct ...
Konrad Rudolph's user avatar
21 votes

What happens if a major bug is discovered in a bioinformatic package that has been used in published literature?

I prefer to treat software tools and computers in a similar fashion to laboratory equipment, and in some sense biology in general. Biologists are used to unexpected things happening in their ...
gringer's user avatar
  • 13.9k
18 votes
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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 ...
Kamil S Jaron's user avatar
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): ...
Konrad Rudolph's user avatar
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: ...
Devon Ryan's user avatar
  • 19.6k
16 votes
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Ultimate reproducibility in R?

You're right about trying to get the R environments to be as similar as possible, as easily as possible. It's not always necessary to have the exact environment to get the same results, but it ...
James Hawley's user avatar
  • 1,384
15 votes
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How to convert species names into common names?

As Pierre mentioned, NCBI is a good resource for this kind of transformation. You can still use taxize to perform the conversion: ...
Iakov Davydov's user avatar
14 votes

How to convert species names into common names?

use the NCBI taxon dump under ftp://ftp.ncbi.nih.gov/pub/taxonomy in taxdmp.zip you'll find all the names for a given NCBI taxon ...
Pierre's user avatar
  • 1,511
13 votes
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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 "...
Devon Ryan's user avatar
  • 19.6k
13 votes

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

I'd like to find genes that were not expressed in a group of samples and were expressed in another group. This is, fundamentally, a differential expression analysis, with a twist. To solve this, you’...
Konrad Rudolph's user avatar
13 votes
Accepted

Using the t-SNE algorithm on microarray data + an error bonus

Converting your data.frame to a matrix (and then removing the data.frame) will often free up ...
Devon Ryan's user avatar
  • 19.6k
13 votes
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Volcano plot in R

This plot is clearly done using core R functions. There are smoother alternatives how to make a pretty volcano plot (like ggplot with example here), but if you ...
Kamil S Jaron's user avatar
12 votes
Accepted

How to make chromosome color maps for bed ranges

You can use karyoploteR to plot your regions on an ideogram quite easily. Disclosure: I'm one of the authors of the tool. For this example I'll start creating 4 GRanges with random regions, but with ...
bernatgel's user avatar
  • 166
12 votes

Converting Gene Symbol to Ensembl ID in R

You can use the standard annotation package for humans (you can also use biomaRt, but it can be more confusing, see below): ...
llrs's user avatar
  • 4,693
11 votes

How do I generate a color-coded tanglegram?

I think you can try dendextend, in this manual there is an example of coloring the branches. I don't think it is exactly like your coloring, but with a little tweaking you might get your colorscheme ...
benn's user avatar
  • 3,571
11 votes
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plotting two heatmaps with the same order of genes

ComplexHeatmap is built for plotting side-by-side heat maps with the same clustering - you use the + notation, similar to ggplot2. To use the same example data as @...
sjcockell's user avatar
  • 861
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 ...
llrs's user avatar
  • 4,693
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 ...
bli's user avatar
  • 3,130
10 votes

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

A common method is to use zFPKMs, which you can find implemented in R here. Having said that, there's an inherent problem in declaring a difference between two things on either side of a given ...
Devon Ryan's user avatar
  • 19.6k
10 votes
Accepted

Determine if a gene is mitochondrial or not

You can't determine if a gene is mitochondrial purely from its name. The simplest route would be to use the wormbase biomart and either download the gene names and their associated chromosomes or use ...
Devon Ryan's user avatar
  • 19.6k
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 ...
Devon Ryan's user avatar
  • 19.6k
10 votes
Accepted

Convert R RNA-seq data object to a Python object

A simple solution for converting Seurat objects into AnnData, as described in this vignette: ...
Peter's user avatar
  • 2,634
9 votes

How to compute RPKM in R?

RPKM is defined as: RPKM = numberOfReads / ( geneLength/1000 * totalNumReads/1,000,000 ) As you can see, you need to have gene lengths for every gene. Let's say ...
Iakov Davydov's user avatar
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 ...
Konrad Rudolph's user avatar
9 votes
Accepted

How to apply upperquartile normalization on RSEM expected counts?

You can use the quantile function in base R to get the value of a particular quantile (e.g. 0.75 for the upper quartile). This can then be used as a factor for ...
gringer's user avatar
  • 13.9k
9 votes

BiomaRt error: Error in martCheck

getSequence has only been enabled for the main Ensembl (vertebrates) biomaRt. This is all at the Bioconductor end. You'll need to use a getBM instead, for example: ...
Emily_Ensembl's user avatar
9 votes

What happens if a major bug is discovered in a bioinformatic package that has been used in published literature?

While I agree with gringer's answer I would first report the bug to the maintainers with a test case (if possible) in order to have the bug corrected. The bug might be an erroneous implementation ...
llrs's user avatar
  • 4,693
9 votes
Accepted

BioMart does not return a result

Whenever you are wondering about things like this, just look up the identifier on the Ensembl web page. If you look up ENSMUSG00000083840, you will see: This ...
terdon's user avatar
  • 9,856
9 votes

How I can change the name of multiple files at once in R or terminal?

Use perl-rename. This is usually called rename on Debian-based systems like Ubuntu or Mint, and ...
terdon's user avatar
  • 9,856
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: ...
llrs's user avatar
  • 4,693

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