scRNAseq | Bioconductor repository for the scRNAseq package | Genomics library

by LTLA R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(6)Vulnerabilities Install Support

kandi X-RAY | scRNAseq Summary

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

Clone of the Bioconductor repository for the scRNAseq package.

Support

Quality

Security

License

Reuse

Support

scRNAseq has a low active ecosystem.

It has 10 star(s) with 9 fork(s). There are 2 watchers for this library.

It had no major release in the last 6 months.

There are 5 open issues and 12 have been closed. On average issues are closed in 41 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of scRNAseq is current.

Quality

scRNAseq has no bugs reported.

Security

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

License

scRNAseq 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

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

Top functions reviewed by kandi - BETA

kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of scRNAseq

Get all kandi verified functions for this library.

scRNAseq Key Features

No Key Features are available at this moment for scRNAseq.

scRNAseq Examples and Code Snippets

No Code Snippets are available at this moment for scRNAseq.

Community Discussions

Trending Discussions on scRNAseq

Not able to install scanpy package using conda install or pip

Error installing R package: scran using Anaconda

R kernel crashes while loading R package using rpy2

How to solve keras fit function error "All input arrays (x) should have the same number of samples"?

Reduce memory usage of a line of code that uses numpy

How to determine at which point in python script step memory exceeded in SLURM

QUESTION

Not able to install scanpy package using conda install or pip

Asked 2021-Jan-13 at 13:41

I have been trying to install scanpy package in anaconda using

...

ANSWER

Answered 2021-Jan-13 at 13:41

In your error log you can see

Source https://stackoverflow.com/questions/65703000

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

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

How to solve keras fit function error "All input arrays (x) should have the same number of samples"?

Asked 2019-Oct-28 at 06:11

I'm following the example of Integrating CITEseq data with Deep Learning. The code worked until the third part of the example, where it is supposed to train the autoencoder. Since I'm new to keras models, I'm basically just copying and pasting the code, so I do not know how the one on the website is working and mine is not.

I've tried changing the fit funcion from

...

ANSWER

Answered 2019-Oct-28 at 06:11

Keras expects the first axis of your input data to be the number of samples. As you said, X_scRNAseq shape is (36280, 8617) and the shape of X_scProteomics is (13, 8617). Keras expects the first axis to be the number of samples which isn't true in this case.

The solution, I believe, is to reshape both X_scRNAseq and X_scProteomics like so:

Source https://stackoverflow.com/questions/58586256

QUESTION

Reduce memory usage of a line of code that uses numpy

Asked 2018-Sep-11 at 06:39

I am using the python library:

https://github.com/ficusss/PyGMNormalize

For normalizing my datasets (scRNAseq) and the last line in the library's file utils.py:

https://github.com/ficusss/PyGMNormalize/blob/master/pygmnormalize/utils.py

uses too much of memory:

...

ANSWER

Answered 2018-Sep-11 at 01:28

I'm putting this as an answer since there's more than will fit in a comment, although it may not be complete. There's two suspicious things - first off percentile should run fine on a 20Gb matrix if your machine has 200Gb of ram available. That's a lot of memory, so start looking into what else might be using it. Start with top - is there another process or is your python program using all of that?

The second suspicious thing is that the documentation for utils.percentile doesn't match it's actual behavior. Here's the relevant bits from the code you've linked to:

Source https://stackoverflow.com/questions/52266003

QUESTION

How to determine at which point in python script step memory exceeded in SLURM

Asked 2018-Sep-08 at 16:58

I have a python script that I am running on a SLURM cluster for multiple input files:

...

ANSWER

Answered 2018-Sep-08 at 16:58

You can get refined information by using srun to start the python scripts:

Source https://stackoverflow.com/questions/52229942

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

Vulnerabilities

No vulnerabilities reported

Install scRNAseq

You can download it from GitHub.

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 .

Find more information at: