Decipher R Package

[Denisha Padley]

Iam sorry to post 3 different errors/issues in a single post but I assume this would be more time-saving. I installed R and RStudio on a remote server to run R script that requires a higher memory space and I need to install a bunch of R packages for microbiome analyses.

Are you using RStudio Server on the remote and what user are you doing the installs under? Do you have sudo privileges? Are you installing from the RStudio package manager, install.packages() within RStudio, from the console or from the R CLI? Have you installed any packages at all? Those are global questions that may help unravel the puzzle.

relate to other packages that haven't been installed. Those can be fixed through the tedious process of installing them separately, bracing for the possibility that the dependencies will have dependencies.

Thanks for your reply and suggestions.

Are you using RStudio Server on the remote and what user are you doing the installs under? Do you have sudo privileges? Are you installing from the RStudio package manager, install.packages() within RStudio, from the console or from the R CLI? Have you installed any packages at all? Those are global questions that may help unravel the puzzle.

No, I installed the regular R and RStudio programs using the sudo password of one of the users who has sudo privilege. The installation was on that person's account, but RStudio is still accessible to other users.

Yes, I installed some packages (e.g., ggplot2, gridExtra, WritXLS, knitr, markdown, reshape2) successfully from either RStudio package manager, install.packages() within RStudio, or the console.

To do so, I have to go back to the admin to use sudo. Is it possible to use the admin password in my account or it has to be from their account knowing that there is more than one person having sudo privilege?

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If you have a query related to it or one of the replies, start a new topic and refer back with a link.

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R statistical programming language. The program is designed to be used with non-destructive workflows for importing, maintaining, analyzing, manipulating, and exporting a massive amount of sequences.

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of...

This should install DECIPHER. MicrobeR is a swiss-army knife of sorts to streamline certain tasks or to help visualize and as such it has quite a long list of dependencies. Running the code below might help fill in any missing dependencies. Note, if you are using an unix operating system it will also download some extra sequencing data.

I was able to instamm MicrobeR but the tutorial is based on a preinstalled data in R so it is a bit confusing to figure out how to import our own files (especially QIIME2 format) and what file to import. Can you explain that?

I think it might be related to missing some part of xcode. You can download the full version from the app store, or if space is an issue, I think you can download just the command line tools via the bash terminal with xcode-select --install.

I am unsure how to resolve this. I am new to docker and normally install my R packages within the R environment and not via the command line. I appreciate any help you can offer so that I install this package in my docker image.

Something was going wrong during the installation. Basically, BiocManager failed to install RCurl, which caused the installation of other dependencies to fail as well. I did not resolve this issue. Instead, I simply copied the one function I needed from the DECIPHER package into my code. This resolved the issue for my purposes, but does not solve the problem I identified here.

The issue seems to present itself as a result of certain packages loading and getting in the way of the IdTaxa function but I can't seem to figure out a workaround. I've noticed that I can sometimes get the IdTaxa function to run if I restart the R session, load the DECIPHER library and run it before loading other libraries. However, even this fails if the last bits of the restart (see below) manage to run before I can run the function.

Thanks for posting the link to these workarounds. I've followed the steps you used via Homebrew. My install path (Step 2) was the same as yours but Step 3 didn't work for me. I restarted RStudio and R. I also tried using these lines from -project.org/openmp:

The recommended way you mention is clearly intended as a workaround which could stop working at any point. Are you planning on updating DECIPHER to use another multithreading package that doesn't require OpenMP support?

Just like the title states, I have a job to build an interactive zonal map for the US, and I have two websites as a reference. These two websites are so similar that it has to be a package at work here, most likely.

Abstract In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity. It is now common to collect or have access to many gigabytes of biological sequences. This has created an urgent need for approaches that analyze sequences in subsets without requiring all of the sequences to be loaded into memory at one time. It has also opened opportunities to improve the organization and accessibility of information acquired in sequencing projects. The DECIPHER package offers solutions to these problems by assisting in the curation of large sets of biological sequences stored in compressed format inside a database. This approach has many practical advantages over standard bioinformatics workflows, and enables large analyses that would otherwise be prohibitively time consuming.

Bioconductor packages are strongly interconnected. A message like Update all/some/none? [a/s/n]: Is saying that you potentially have older versions of packages installed and asking if you would like to update any package that has a newer version number. Generally we would recommend a for all but if you are on limited internet capabilities or really eager to get working maybe do n for none and update at a time that is more convenient. Package work best when all are in their current state.

In this worshop we will be walking through a comparative genomics pipeline using functions within the R package DECIPHER, and within a package that is currently under construction under the name FindHomology.

Whereas Lipid construction in eucharyotes and prokaryotes relies on iterative incorporation of malonyl-CoA units, archaea utilize the melvonate pathway to construct their lipids through iterative incorporation of dimethylallyl pyrophosphate. Which is responsible for the iterative methyl groups extant to the lipid chain in B above. Archaeal lipids are also notable for their lack of ester linkages between the alkyl chain, and glyerol. Even more interesting, and as yet uncharacterized, Archaea incorporate a range of ring structures into their lipids, and additionally appear to fuse lipid tails together in the bilayer, as shown above in C.

Our goal with this workshop is to show how functions within DECIPHER, in addition to those found within FindHomology can be used to predict homologs between genomes, as well as predict the core genome of a given set of genomes. As stated above, the chemistry and biology involved in some of the construction of archaeal lipids is unknown. Hypothetically, as this chemistry is universal in these organisms, the genes responsible could all be homologs, and be identified as part of the core genome. Further we can compare the core and pan genomes of this set.

To begin with, we will load the required packages: DECIPHER and FindHomology will provide tools to complete the phylogenetic analysis, while phytools will provide visualization tools, specifically for the visualization of tangelograms, and stringr is used for a specific string operation.

We have now loaded in a character vector for ftp addresses for genomic fasta files GenomeAdds, a character vector of ftp addresses for genomic GFF files GeneCallAdds that we will be using to collect gene boundaries, strandedness, and annotations. And lastly a vector of abbreviated names for the genomes we are working with.

If you choose to mimic this work on your own, there are a few ways to get gene calls(the gene boundaries, and strandedness), and annotations, such as Prodigal29 (for gene calls) and Prokka30 (for annotations). Using the NCBI annotations is simple and conducive for this workshop. However if you are working on sequence data that you have generated or collected yourself, NCBI annotations will not be available. Additionally, a Gene Caller within the DECIPHER package is currently under construction.

Use of databases also allows for a non-destructive workflow. Sequence data in the database can be accessed as needed, but cannot be accidentally manipulated. Databases are also shareable, allowing for accession by multiple users at once.

In your own work, it can be inadvisable to use tempfile() to specify the location of your .sqlite file, especially if it will be a file you use repeatedly, or takes a significant amount of time to create, or that you will eventually need to share with collaborators. However for this workhshop, it is fine.

Comparison of genomes will be accomplished with Synteny. Generically when regions in a genome are the same, they are syntenic matches. Often observing this phenomenon is accomplished through matching runs of reciprocal best blast hits. If in genome 1, genes A-B-C are reciprocal best blast hits to genes Z-Y-X in genome 2, the region encompassing those genes would be considered syntenic.

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