ldsc | LD Score Regression | Analytics library

by bulik Python Version: 2.0.1 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | ldsc Summary

ldsc is a Python library typically used in Analytics applications. ldsc has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install ldsc' or download it from GitHub, PyPI.

ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.

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Quality

Security

License

Reuse

Support

ldsc has a low active ecosystem.

It has 480 star(s) with 293 fork(s). There are 29 watchers for this library.

It had no major release in the last 12 months.

There are 231 open issues and 104 have been closed. On average issues are closed in 105 days. There are 10 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ldsc is 2.0.1

Quality

ldsc has 0 bugs and 0 code smells.

Security

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

ldsc code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ldsc is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

ldsc 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.

ldsc saves you 1789 person hours of effort in developing the same functionality from scratch.

It has 3955 lines of code, 330 functions and 17 files.

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

Top functions reviewed by kandi - BETA

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

Annotate a list of files
Parse annotation file
Return a list of chromosomes present in fh
Parse MF header file
Estimate H2
Print the covariance matrix
Checks the LD score matrix condition
Calculate the overlap output
Estimate genotype parameters
Check if arguments are the same length
Make annotation files
Combine two joint objective functions
Concatenate ld score from a list of files
Make a bedtool for a gene set
Read cts file
Compute the weight matrix for the fitting function
Calculate the weights for the model
Convert an array of block values to the largest block
Print a summary of the SNPs
Delete values from x and y
Summarize the correlation coefficient
Compute the delete values for each block
Compute the block - wise quadrature values
Return a summary of the model
Compute cell type specific
Updates the weights for the model

Get all kandi verified functions for this library.

ldsc Key Features

No Key Features are available at this moment for ldsc.

ldsc Examples and Code Snippets

No Code Snippets are available at this moment for ldsc.

Community Discussions

Trending Discussions on ldsc

Snakemake - Many to one using an expand exception

QUESTION

Snakemake - Many to one using an expand exception

Asked 2018-Dec-21 at 09:37

I have a functioning Snakefile for Partitioned Heritability using multiple bed files. This produces a perfect list of jobs using snakemake -np so this file only needs a minor tweak (I hope!).

My issue occurs in the merge_peaks rule below.

At this stage, I have 25 bed files and need to run 5 calls of merge_peaks, one call for each extension ext=[100,200,300,400,500], so I need only the 5 bed files containing the relevant extension to be called each time.

For example for the following merge_peaks output file peak_files/Fullard2018_peaks.mrgd.blrm.100.bed, I only need the following 5 bed files with ext=100 to be used as input:

...

ANSWER

Answered 2018-Dec-19 at 17:17

I have a solution for this using double curly brackets as an escape character. This works and gives me what I need, but there is still something going on that I don't understand.

So for the input line to the merge_peaks rule instead of:

Source https://stackoverflow.com/questions/53852874

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

Vulnerabilities

No vulnerabilities reported

Install ldsc

In order to download ldsc, you should clone this repository via the commands.

Support

Before contacting us, please try the following:. If that doesn't work, you can get in touch with us via the google group. Issues with LD Hub? Email ld-hub@bristol.ac.uk.

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