SingleCellExperiment | Bioconductor repository | Genomics library

by drisso R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | SingleCellExperiment Summary

SingleCellExperiment is a R library typically used in Artificial Intelligence, Genomics applications. SingleCellExperiment has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

This is a clone of the Bioconductor repository for the SingleCellExperiment package.

Support

Quality

Security

License

Reuse

Support

SingleCellExperiment has a low active ecosystem.

It has 47 star(s) with 15 fork(s). There are 5 watchers for this library.

It had no major release in the last 6 months.

There are 4 open issues and 36 have been closed. On average issues are closed in 8 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of SingleCellExperiment is current.

Quality

SingleCellExperiment has no bugs reported.

Security

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

License

SingleCellExperiment 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

SingleCellExperiment releases are not available. You will need to build from source code and install.

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

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SingleCellExperiment Key Features

No Key Features are available at this moment for SingleCellExperiment.

SingleCellExperiment Examples and Code Snippets

No Code Snippets are available at this moment for SingleCellExperiment.

Community Discussions

Trending Discussions on SingleCellExperiment

Is R looking for a function that is not there?

Error installing R package: scran using Anaconda

Cannot create SingleCellExperiment object after convert 'SYMBOL' to 'NCBI ID'

R kernel crashes while loading R package using rpy2

Create named list from matrix using rpy2

QUESTION

Is R looking for a function that is not there?

Asked 2020-May-26 at 13:05

I'm having a weird issue with R.

Basically, I am following this analysis pipeline in order to understand how it works. At some point (right after the first introductory paragraph, the last few lines of the history) I find this piece of code:

...

ANSWER

Answered 2020-Apr-16 at 11:10

This is the default R behaviour.

If you call a not imported or non-existing function, the error message looks like:

Source https://stackoverflow.com/questions/61247055

QUESTION

Error installing R package: scran using Anaconda

Asked 2020-Apr-06 at 15:18

I am using anaconda to download an R package called scran. Although I have download it to my R library path, I received error. When I try to load my package in my R environment, it also failed. I am on macOS Catalina (10.15.4). I also try BiocManager::install(scran), but also failed.

scran (https://bioconductor.org/packages/release/bioc/html/scran.html)

Can someone give me a hand? Really appreciated! Please see the details below.

# I download scran using conda install -c Bioconda bioconductor-scran

...

ANSWER

Answered 2020-Apr-06 at 15:18

I had your exact second error you are experiencing today, and think I have found a fix.

After doing some digging, I found my problem was with openblas not SCRAN. My fix was:

Source https://stackoverflow.com/questions/61056386

QUESTION

Cannot create SingleCellExperiment object after convert 'SYMBOL' to 'NCBI ID'

Asked 2020-Jan-31 at 13:32

I follow the online scTensor tutorial to analyze the 10x Genomics data from pig. After I convert 'SYMBOL' to 'NCBI ID', I cannot create SingleCellExperiment object. If I don't do the conversion, there is not any problem. Could you help me to figure it out? Thank you.

...

ANSWER

Answered 2020-Jan-31 at 13:32

You have the error because when you map the names, it is a named vector you are assigning as rownames of the matrix. Try this below:

So let's say we have a count table like below:

Source https://stackoverflow.com/questions/59922402

QUESTION

R kernel crashes while loading R package using rpy2

Asked 2020-Jan-06 at 01:16

First of all, I’m new to rpy2 / jupyter so please don’t judge me if this isn’t the correct place to ask my question.

I am trying to set up an integrated workflow for data analysis using R and Python and I encounter the following error:

I am on Ubuntu 19.04. running a conda environment using Jupyter 1.0.0, Python 3.7.4, R 3.5.1, r-irkernel 1.0.2 and rpy2 3.1.0 and I installed the R-package Seurat through R.

When I create a Jupyter notebook using the R-kernel, I can load Seurat with library(Seurat) just fine.

I can also use R code in python using rpy2 and the rmagic such as:

...

ANSWER

Answered 2019-Nov-02 at 15:29

The R package Seurat is using an other R package called reticulate, providing a bridge to Python from R.

Unfortunately, whenever rpy2 and reticulate are involved R ends up being initialized twice, which results inevitably in a segfault. This is still an open bug at the time of writing. The issue tracking on the rpy2 side (a link to the reticulate side of the tracking can be found there) is here:

https://bitbucket.org/rpy2/rpy2/issues/456/reticulate-rpy2-sharing-r-process

Source https://stackoverflow.com/questions/58611486

QUESTION

Create named list from matrix using rpy2

Asked 2018-Sep-12 at 19:51

I have a 2D numpy array which I converted to R matrix and now I need to convert it further to named list:

...

ANSWER

Answered 2018-Sep-12 at 19:51

Ultimately I solved it (avoiding convertion of numpy array to r matrix), straight making the named list from the numpy array:

Source https://stackoverflow.com/questions/52284320

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install SingleCellExperiment

Please, see the SingleCellExperiment Bioconductor page for details on how to install and use the package.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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