GSEApy | Gene Set Enrichment Analysis in Python | Genomics library

by zqfang Python Version: v1.0.4 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | GSEApy Summary

GSEApy is a Python library typically used in Artificial Intelligence, Genomics applications. GSEApy has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. However GSEApy has 2 bugs. You can download it from GitHub.

Gene Set Enrichment Analysis in Python

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Quality

Security

License

Reuse

Support

GSEApy has a low active ecosystem.

It has 392 star(s) with 97 fork(s). There are 9 watchers for this library.

It had no major release in the last 12 months.

There are 11 open issues and 131 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 GSEApy is v1.0.4

Quality

GSEApy has 2 bugs (0 blocker, 0 critical, 1 major, 1 minor) and 182 code smells.

Security

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

GSEApy code analysis shows 0 unresolved vulnerabilities.

There are 12 security hotspots that need review.

License

GSEApy is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

GSEApy releases are available to install and integrate.

Build file is available. You can build the component from source.

GSEApy saves you 1044 person hours of effort in developing the same functionality from scratch.

It has 2369 lines of code, 123 functions and 13 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed GSEApy and discovered the below as its top functions. This is intended to give you an instant insight into GSEApy implemented functionality, and help decide if they suit your requirements.

Run Enrichr
enrich the background
Query gene ids
Return the set of background genes
Generate a tensorflow tensorflow problem
Compute the FDR distribution
Compute the significance of a GSE
Compute the p - value p - value
Run the analysis
Compute the heatmatrix for each phenotype
Load genesets from gmt
Load a Gmt file into memory
Compute the fitness scores for the given gene
Generate a ranking metric tensor
Calculate enrichment score tensor
Plot ring plot
Save the figure
Read a gmt file
Prepare the output directory for gseapy
Prepare the outdir for the gene_set
Run SSGSEA analysis
Plot a histogram of values
Creates an argument parser
Run prerank analysis
Query gene identifiers
Set the organism name
Find the python version string

Get all kandi verified functions for this library.

GSEApy Key Features

No Key Features are available at this moment for GSEApy.

GSEApy Examples and Code Snippets

No Code Snippets are available at this moment for GSEApy.

Community Discussions

Trending Discussions on GSEApy

Best way for installing non-conda dependencies in Snakemake conda environments

Is it possible to check the OS compatibility of a conda .yaml file?

QUESTION

Best way for installing non-conda dependencies in Snakemake conda environments

Asked 2020-Nov-02 at 20:30

I would like to be able to install R packages from GitHub in a R conda environment created by Snakemake, as well as python libraries via pip in a python environment. I'll use these environments in a whole set of rules thereafter.

My initial thought was to create a rule running a script to install the specified packages.

For instance, my initial run was: snakemake -j1 --use-conda -R create_r_environment.

My Snakefile:

...

ANSWER

Answered 2020-Nov-01 at 09:18

I think there are quite a few wrong things:

remotes::install_github("ramiromagno/gwasrapidd", upgrade = "never"): In your r.yaml you should include the remotes package.
!pip install gseapy is not valid python code. If anything, it is code to be executed by shell but I'm not sure that leading ! is correct. Also, gseapy is available from bioconda I don;t see why you should install it with pip.

Before OP edited the question

My envs/r.yaml file:

Source https://stackoverflow.com/questions/64617670

QUESTION

Is it possible to check the OS compatibility of a conda .yaml file?

Asked 2020-Jul-21 at 04:09

Given a .yaml file such as

...

ANSWER

Answered 2020-Jul-21 at 04:09

Automatically? No, not in terms of a built-in CLI option for that purpose. But one could parse out all the package names (e.g., via grep/awk/sed), then check each of them with conda search. The trick to check platform-specific branches in Anaconda Cloud repositories is to use the subdir key for whatever platform you are validating for. For example,

Source https://stackoverflow.com/questions/62996112

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

Vulnerabilities

No vulnerabilities reported

Install GSEApy

You can download it from GitHub.
You can use GSEApy like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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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