deepTools | Tools to process and analyze deep sequencing data | Genomics library

by deeptools Python Version: 3.5.5 License: Non-SPDX

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

kandi X-RAY | deepTools Summary

deepTools is a Python library typically used in Artificial Intelligence, Genomics applications. deepTools has no bugs, it has no vulnerabilities, it has build file available and it has low support. However deepTools has a Non-SPDX License. You can install using 'pip install deepTools' or download it from GitHub, PyPI.

Tools to process and analyze deep sequencing data.

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Quality

Security

License

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Support

deepTools has a low active ecosystem.

It has 574 star(s) with 198 fork(s). There are 36 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 107 open issues and 764 have been closed. On average issues are closed in 54 days. There are 7 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of deepTools is 3.5.5

Quality

deepTools has 0 bugs and 0 code smells.

Security

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

deepTools code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

deepTools has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

deepTools releases are available to install and integrate.

Deployable package is available in PyPI.

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

Installation instructions, examples and code snippets are available.

deepTools saves you 8974 person hours of effort in developing the same functionality from scratch.

It has 18583 lines of code, 418 functions and 83 files.

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

Top functions reviewed by kandi - BETA

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

Plot a heatmap matrix
Return a list of regions
Get the matrix for a group
Flatten the matrix
Calculate coverage of a region in regions
Returns the length of a read
Return the chroms associated with a given chromosome or chromosome
Compute the matrix
Remove regions that are empty
Map a function to each chromosome
Filters out reads that match chromosome
Apply a function to a mapReduce
Parse the command line arguments
Parse command line arguments
Plot the profile
Plot the matrix
Plot the heatmap
Return the fragment portion of a read
Plot the correlation matrix
Plot the PCA matrix
Get read and fragment length from a BAM file
Creates a worker function for filtering reads
Calculate fragment size
Sort region matrix
Plot a correlation matrix
Plot enrichment of features
Calculate the score per chromosome

Get all kandi verified functions for this library.

deepTools Key Features

No Key Features are available at this moment for deepTools.

deepTools Examples and Code Snippets

No Code Snippets are available at this moment for deepTools.

Community Discussions

Trending Discussions on deepTools

Cannot run program using system() in R

How to fix deeptoolsintervals fatal error: Python.h?

QUESTION

Cannot run program using system() in R

Asked 2021-Mar-23 at 18:29

I am trying to run computeMatrix from the package deepTools in a R script using system().

The following command gets this error message.

system('computeMatrix --help')

sh: computeMatrix: command not found
Warning message:
In system("computeMatrix --help") : error in running command

However, if I run the same command in the terminal everthing works fine.

sessionInfo()

R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

...

ANSWER

Answered 2021-Mar-23 at 18:29

This was run in Ubuntu 20.04.
The recommended way of running system commands is with system2, not system. The arguments are passed in a vector, args. In this case args is a length 1 vector but if there are more than one argument, pass them as

Source https://stackoverflow.com/questions/66767864

QUESTION

How to fix deeptoolsintervals fatal error: Python.h?

Asked 2021-Mar-09 at 12:51

I tried installing pip3 install deeptoolsintervals the error is:

...

ANSWER

Answered 2021-Mar-09 at 12:51

the problem was that I was not using the same version of python each time, so I installed the python-env for python3.9

Source https://stackoverflow.com/questions/66546716

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

Vulnerabilities

No vulnerabilities reported

Install deepTools

deepTools are available for:.
Command line usage (via pip/anaconda/github)
Integration into Galaxy servers (via toolshed/API/web-browser)
deepTools can be easily integrated into Galaxy. Please see the installation instructions in our documentation for further details. Note: From version 2.3 onwards, deepTools support python3. This tool suite is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg. Documentation | deepTools Galaxy | FAQ.

Support

Our documentation contains more details on the individual tool scopes and usages and an introduction to our deepTools Galaxy web server including step-by-step protocols. Please see also the FAQ, which we update regularly. Our Gallery may give you some more ideas about the scope of deepTools. For more specific troubleshooting, feedback, and tool suggestions, please post to Biostars.

Find more information at: