WGCNA | : exclamation : This is a read-only mirror of the CRAN R | Development Tools library

by cran R Version: Current License: No License

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kandi X-RAY | WGCNA Summary

WGCNA is a R library typically used in Utilities, Development Tools applications. WGCNA has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

WGCNA

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Quality

Security

License

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Support

WGCNA has a low active ecosystem.

It has 34 star(s) with 48 fork(s). There are 5 watchers for this library.

It had no major release in the last 6 months.

WGCNA has no issues reported. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of WGCNA is current.

Quality

WGCNA has 0 bugs and 0 code smells.

Security

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

WGCNA code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

WGCNA 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

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

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WGCNA Key Features

No Key Features are available at this moment for WGCNA.

WGCNA Examples and Code Snippets

No Code Snippets are available at this moment for WGCNA.

Community Discussions

Trending Discussions on WGCNA

How to load Seurat Object into WGCNA Tutorial Format

Does the order of a HClust object give the order in which the labels are appearing on a tree?

How can I use broadcasting with NumPy to speed up this correlation calculation?

WGCNA : Choosing a soft-threshold power

QUESTION

How to load Seurat Object into WGCNA Tutorial Format

Asked 2021-Aug-22 at 23:27

As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA (https://ucdavis-bioinformatics-training.github.io/2019-single-cell-RNA-sequencing-Workshop-UCD_UCSF/scrnaseq_analysis/scRNA_Workshop-PART6.html). I am really new to programming so it's probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA's tutorials (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/).

Here is what I have tried thus far:

This tries to replicate datExpr and datTraits from part I.1:

...

ANSWER

Answered 2021-Aug-22 at 23:27

So doing as.matrix(datExpr) right after datExpr <- t(sobjwgcnamat)[,VariableFeatures(sobjwgcna)] worked. I had been trying it right before MEList = moduleEigengenes(datExpr, colors = moduleColors) and that didn't work. Seems simple but order matters I guess.

Source https://stackoverflow.com/questions/68853859

QUESTION

Does the order of a HClust object give the order in which the labels are appearing on a tree?

Asked 2021-May-19 at 16:49

I'm doing WGCNA on expression data and I performed a clustering using the hclust function:

...

ANSWER

Answered 2021-May-19 at 16:49

Here is a test using part of the iris data set to see if the labels match:

Source https://stackoverflow.com/questions/67584062

QUESTION

How can I use broadcasting with NumPy to speed up this correlation calculation?

Asked 2020-Apr-15 at 18:10

I'm trying to take advantage of NumPy broadcasting and backend array computations to significantly speed up this function. Unfortunately, it doesn't scale so well so I'm hoping to greatly improve the performance of this. Right now the code isn't properly utilizing broadcasting for the computations.

I'm using WGCNA's bicor function as a gold standard as this is the fastest implementation I know of at the moment. The Python version outputs the same results as the R function.

...

ANSWER

Answered 2020-Apr-07 at 23:52

With a copy-n-paste of your X:

Source https://stackoverflow.com/questions/61090539

QUESTION

WGCNA : Choosing a soft-threshold power

Asked 2020-Feb-18 at 08:43

powers = c(c(1:10), seq(from = 12, to=20, by=2));

While going through WGCNA i came across this code which i am not able to understand, can anybody explain me the meaning of that piece of code

...

ANSWER

Answered 2020-Feb-18 at 08:43

The code will create a vector of numbers stored in powers.

Specifically: 1:10 creates the numbers 1 2 3 4 5 6 7 8 9 10 (can read as 1 through 10) and seq(from = 12, to = 20, by = 2) creates a sequence of every other number from 12 to 20, i.e. 12 14 16 18 20.

Powers will contain the following 15 numbers: 1 2 3 4 5 6 7 8 9 10 12 14 16 18 20

I am not familiar with the WGCNApackage or if powers is an argument to a function, but this is what powers contains.

Source https://stackoverflow.com/questions/60274874

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

Vulnerabilities

No vulnerabilities reported

Install WGCNA

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 .

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