Xvector Package

[Regulo Akers]

Iam trying to work on a fas extension file with using 'Biostrings' package. I have attempted a multiple different ways, exhausted google searches without much success on different webs/blogs/video tutorials.

I probably found an answer. Not quite sure if I can answer my own question. First, both comments by @Maurits and @Poshi were right. I appreciate them again. It's probably a longer version of what they wisely mentioned above, but my thought process is below. This is for other beginners who might fall into same misunderstanding that I went through... to save their time and energy.

First, the fas (or fasta, fa) files are essentially the same, if the file creator did not intend to fool the user by putting a different extension on purpose. One way to know whether it truly is based on the same format is, just by opening them in any ASCII text editor or equivalent environment and browse the first few lines. However, beware if the file size is huge, it will consume your RAM and make your computer uncomfortable.

Second, I checked whether the file truly contains the definition line as well as the sequence. I know it's a blunt way (and may not be totally accurate), but even before I went to ASCII level, I opened it on R with below:

Third, understand the fas (or fasta) can store all sequence in one line. It's basically a complex form of a list, and your sequence can be stored in different ways, but contiguous bases usually need not to be stored fragmented. So my sequence was all in one line!

I've been trying to install DESeq2 for differential expression analysis. Unfortunately, installation keeps failing because the dependencies can not be installed. The culprit is the XVector package, that is required for one of DESeq2's dependencies. This is the error:

Due to this zlib.h file that is not found, the installation fails. I'm working in rstudio hosted from a docker container based on the rocker/rstudio:4.0.5 (newer versions like 4.1.1 throw the same error). Installing zlib by running sudo apt-get install zlib1g in the docker container does not solve the problem, as zlib1g is already installed with the newest version.

If you are extending a rocker/rstudio image you should install the development version of some libraries (only they contain the header files which are needed to build the R-packages) and two additional libraries:

Thanks for your answer, this indeed solves my problem. Initially when I tried your solution I ran into several errors relating to packages that are not available. I learned that apt-get update needs to be run in the rocker/rstudio based container to find the packages. Next I could run apt-get install zlib1g-dev to solve the problem that occurred with XVector and apt-get install libxml2-dev to deal with another error that would otherwise occur, for reference:

Using R 4.1.2 (from the rocker/rstudio:4.1.2 docker image) results in the same problem as the other version. I tried using the bioconductor image (bioconductor/bioconductor_docker:latest) and this works without issues. I noticed that this docker container uses 4.3GB of disk space, while the previous containers end up using about 2.3GB. However, that is fine for me at the moment.

@swaiba - installing Biostrings will automatically identifiy and update all needed packages - this is not something you need to worry about directly. The root cause of your problem that prevents you to install Biostrings is that you are missing some software provided by the Linux OS, i.e. zlib.h.

You can solve the problem by running yum install zlib-devel on a RedHat Enterprise Linux based system or by running apt-get install zlib1g-dev on an Debian/Ubuntu based system. Once you installed this, the installation of Biostrings should be successful.

You also could use pak::pkg_install("Biostrings") which will install Biostrings as well - it will also tell you if any operating system dependencies (e.g. zlib.h) are missing - if run with admin privilegs, pak will automatically install those operating system dependencies for you.

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Lenti-X Packaging Single Shots (Integrase Deficient) provide a one-step production method to generate high-titer lentivirus. Each tube of Lenti-X Packaging Single Shots (Integrase Deficient) contains pre-measured, lyophilized Xfect Transfection Reagent and an optimized formulation of Lenti-X lentiviral packaging plasmids. High-titer, integrase-deficient lentivirus is produced by adding the lentiviral vector of choice in sterile water to the tube, reconstituting, and then using the mixture to transfect 293T cells (e.g., Lenti-X 293T Cell Line, Cat. # 632180) in a 10-cm dish.

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