BiocManager | CRAN Package For Managing Bioconductor Packages | Data Visualization library

by Bioconductor R Version: v1.30.19 License: No License

X-Ray Key Features Code Snippets(3)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | BiocManager Summary

BiocManager is a R library typically used in Analytics, Data Visualization applications. BiocManager has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

The BiocManager package, as the modern successor package to BiocInstaller, allows users to install and manage packages from the Bioconductor project. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data. Current Bioconductor packages are available on a ‘release’ version intended for every-day use, and a ‘devel’ version where new features are continually introduced. A new release version is created every six months. Using the BiocManager package helps users accurately install packages from the appropriate release.

Support

Quality

Security

License

Reuse

Support

BiocManager has a low active ecosystem.

It has 58 star(s) with 17 fork(s). There are 16 watchers for this library.

It had no major release in the last 12 months.

There are 19 open issues and 92 have been closed. On average issues are closed in 66 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of BiocManager is v1.30.19

Quality

BiocManager has 0 bugs and 0 code smells.

Security

BiocManager has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

BiocManager code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

BiocManager does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

BiocManager releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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BiocManager Key Features

No Key Features are available at this moment for BiocManager.

BiocManager Examples and Code Snippets

BiocManager,Usage,Verifying a valid Bioconductor installation

Lines of Code : 40

License : No License

Copy

BiocManager::valid()
#> Warning: 0 packages out-of-date; 1 packages too new
#> 
#> * sessionInfo()
#> 
#> R Under development (unstable) (2019-10-07 r77258)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.04

BiocManager,Installation

Lines of Code : 2

License : No License

Copy

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager,Usage,Checking Bioconductor version currently installed

Lines of Code : 2

License : No License

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BiocManager::version()
#> [1] '3.11'

Community Discussions

Trending Discussions on BiocManager

Problems installing older version of Bioconductor's mixOmics packages in R

External dendrogram does not keep the same formation when using it for cluster_rows in complexheatmap

Can you silently install Bioconductor packages?

Why do results differ for dplyr left_join() and right_join() using these two dataframes

Add API endpoint to invoke AWS Lambda function running docker

Snakemake installing R package in rule environment: error cannot move 00LOCK permission denied

How to add multiple pdata identities of same type to one sample, and be able to distinguish by those identities when plotting

How to add additional statistics on top of a combined ggplot2 graph that uses a multi-variable object or two separate objects

Non standard evaluation does not work: Error in h(simpleError(msg, call))

image to csv and to dataset of multiple images in R

QUESTION

Problems installing older version of Bioconductor's mixOmics packages in R

Asked 2022-Feb-25 at 04:17

I've spent the day trying to load the appropriate package versions in R that I saved in a renv lockfile.

I used the package RVAideMemoire which is tied in with mixOmics in bioconductor, which can't be loaded automatically using renv::restore().

I followed the steps outlined here to install the appropriate version of bioconductor (3.11) to get moxOmics version 6.12.1.

R how to install a specified version of a bioconductor package?

Unfortunately I ended up with mixOmics version 6.14.1. I attempted to load the earlier version using:

...

ANSWER

Answered 2022-Feb-25 at 04:17

BiocManager::install() doesn't provide an interface for installing specific versions of a package. The documentation for the version argument states:

version: 'character(1)' Bioconductor version to install, e.g., 'version = "3.8"'. The special symbol 'version = "devel"' installs the current 'development' version.

That is, it relates to the Bioconductor version, not the package version.

That said, you should be able to use renv to install a specific version of the package from Bioconductor. For example:

Source https://stackoverflow.com/questions/71247393

QUESTION

External dendrogram does not keep the same formation when using it for cluster_rows in complexheatmap

Asked 2022-Feb-04 at 11:21

I am trying to create a heatmap with an external dendrogram using the ComplexHeatmap library .

...

ANSWER

Answered 2022-Feb-04 at 11:21

The problem is that after all the transformations:

Source https://stackoverflow.com/questions/70956152

QUESTION

Can you silently install Bioconductor packages?

Asked 2022-Jan-25 at 14:49

I'm writing a pipeline in Snakemake that calls an R script. This R script has its own environment, with r-base, r-ggplot2 and r-biocmanager in it. I also need the package ggbio that can be installed with biocmanager. I want to silently install this package when the script is called because I don't want it to flood my terminal. Is there a way to do this? I have this right now, but this still outputs instalment information to the terminal:

...

ANSWER

Answered 2022-Jan-24 at 20:34

If you must install the package quietly you can do:

Source https://stackoverflow.com/questions/70243314

QUESTION

Why do results differ for dplyr left_join() and right_join() using these two dataframes

Asked 2021-Dec-31 at 11:12

I am learning how to use the R dplyr 'join' functions by doing the exercises from this course: https://github.com/uclouvain-cbio/WSBIM1207 and got stuck on the problem described below.

First, download the example dataframes used for this question:

...

ANSWER

Answered 2021-Dec-31 at 11:12

Update Maybe not clearly explained. Here an explanation with the original data:

create left join

Source https://stackoverflow.com/questions/70536460

QUESTION

Add API endpoint to invoke AWS Lambda function running docker

Asked 2021-Dec-17 at 20:47

Im using Serverless Framework to deploy a Docker image running R to an AWS Lambda.

...

ANSWER

Answered 2021-Dec-15 at 23:26

The way your events.http is configured looks wrong. Try replacing it with:

Source https://stackoverflow.com/questions/70297377

QUESTION

Snakemake installing R package in rule environment: error cannot move 00LOCK permission denied

Asked 2021-Dec-07 at 17:36

I'm writing a Snakemake pipeline with a rule that will run an R script. This rule has its own environment that looks like this:

...

ANSWER

Answered 2021-Dec-07 at 17:36

The YAML shown is substandard (incorrect channel order). But more importantly, it generally does not work well to install anything other than Conda packages in Conda-managed R environments. Fortunately, all Bioconductor packages are on the bioconda channel (usually with a bioconductor- prefix and all lowercase), hence, everything should work perfectly fine with simply:

Source https://stackoverflow.com/questions/70262630

QUESTION

How to add multiple pdata identities of same type to one sample, and be able to distinguish by those identities when plotting

Asked 2021-Jul-02 at 16:33

I am trying to essentially add phenotypic information (pdata) to a sample in this dataset.

...

ANSWER

Answered 2021-Jul-02 at 16:33

See https://github.com/satijalab/seurat/issues/4650 . It looks like I need the batch information for each cell if I want to plot it in the way that I am.

Source https://stackoverflow.com/questions/68023848

QUESTION

How to add additional statistics on top of a combined ggplot2 graph that uses a multi-variable object or two separate objects

Asked 2021-Jun-22 at 07:09

I have a ggplot2 graph which plots two separate violin plots onto one graph, given by this example (thanks to @jared_mamrot for providing it):

...

ANSWER

Answered 2021-Jun-17 at 20:43

for you to be able to use the data within a plot without specifying it (like geom_boxplot() ), you need to put the data in the ggplot() function call. Then the following functions are able to inherit them.

You also do not need an extra violin plot per color

Source https://stackoverflow.com/questions/68025965

QUESTION

Non standard evaluation does not work: Error in h(simpleError(msg, call))

Asked 2021-Jun-02 at 07:38

Here is a working example of what I want to do.

...

ANSWER

Answered 2021-Jun-02 at 07:37

A solution offered by the authors of the phyloseq package:

Source https://stackoverflow.com/questions/67705772

QUESTION

image to csv and to dataset of multiple images in R

Asked 2021-May-15 at 06:47

I am attempting to do some image recognition on pokemon images and I have downloaded a file folder with many images of pokemon. I have library EBImage fro the BiocManager package and used it to create an image into a csv using the code below. But, is there a way to automate this with a for loop maybe and call in all of the images in the folder?

...

ANSWER

Answered 2021-May-15 at 06:47

You can try :

Source https://stackoverflow.com/questions/67541312

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