SCHISM | Subclonal Hierarchy Inference from Somatic Mutations | Machine Learning library

by KarchinLab Python Version: SCHISM-1.1.3 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | SCHISM Summary

SCHISM is a Python library typically used in Artificial Intelligence, Machine Learning applications. SCHISM has no bugs, it has no vulnerabilities, it has build file available and it has low support. However SCHISM has a Non-SPDX License. You can download it from GitHub.

SCHISM is a computational tool designed to infer subclonal hierarchy and the tumor evolution from somatic mutations. The inference process involves computational assessment of two fundamental properties of tumor evolution: lineage precedence rule and lineage divergence rule. First, SCHISM combines information about somatic mutation cellularity (aka mutation cancer cell fraction) across all tumor sample(s) available from a patient in a hypothesis testing framework to identify the statistical support for the lineage relationship between each pair of mutations or mutation clusters. The results of the hypothesis test are represented as Cluster Order Precedence Violation (CPOV) matrix which informs the subsequent step in SCHISM and ensures compliance of candidate tree topologies with lineage precedence rule. Next, an implementation of genetic algorithm (GA) based on a fitness function that incorporates considerations for both lineage precedence (CPOV) rule and lineage divergence rule explores the space of tree topologies and returns a prioritized list of candidate subclonal phylogenetic trees, most compatible with observed cellularity data.

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Support

SCHISM has a low active ecosystem.

It has 18 star(s) with 5 fork(s). There are 6 watchers for this library.

It had no major release in the last 12 months.

There are 5 open issues and 1 have been closed. On average issues are closed in 5 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of SCHISM is SCHISM-1.1.3

Quality

SCHISM has 0 bugs and 0 code smells.

Security

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

SCHISM code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

SCHISM 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

SCHISM releases are available to install and integrate.

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

SCHISM saves you 785 person hours of effort in developing the same functionality from scratch.

It has 1806 lines of code, 102 functions and 10 files.

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

Top functions reviewed by kandi - BETA

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

Prepare inputs for hypothesis testing
Generate a cellularity file
Generate a cellularity file for each mutation
Read a mutation count file
Run GA workflow
Add new generations to the tree
Returns a list of nObjects
Sum the number of items in a list
Test the hypothesis test
Combine the KL statistic
Determines the outcome of the test
Store the HTT decision matrix
Generate consensus consensus tree
Given a list of nwkFittest trees returns a list of unique edge pairs
Performs the clustering
Cluster mutations using DBscan
Cluster vm
Builds a vote matrix from a pov matrix
Integrate cluster metrics
Calculate the mass cost for each child
Summarize summary statistics
Merge the GA trace file
Read an instance

Get all kandi verified functions for this library.

SCHISM Key Features

No Key Features are available at this moment for SCHISM.

SCHISM Examples and Code Snippets

No Code Snippets are available at this moment for SCHISM.

Community Discussions

Trending Discussions on SCHISM

How do lisps that prefer first and rest to car and cdr approach combinations like cdaddr?

How can I use conditionals in python to solve the code shown below?

Adding data to a Dict

QUESTION

How do lisps that prefer first and rest to car and cdr approach combinations like cdaddr?

Asked 2021-Jan-30 at 15:38

One of the great schisms in the Lisp community is if we should have car and cdr or first and rest. One of the benefits of the traditional car and cdr is that we can combine them to produce pronoucible functions like cdaddr. How do Lisps that do not use car and cdr, such as Clojure, typically form combinations like this with first and rest? Is there any consensus?

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ANSWER

Answered 2021-Jan-30 at 15:38

Clojure, at any rate, simply has no need for caddaadr and friends, because nobody builds data structures out of just cons cells. The language does have combinations of any two of first and next, named ffirst, fnext, nnext, and nfirst, which were added very early on I suppose because it was assumed we'd want something like cadr, but I never see them used in real life. Instead destructuring is used quite often.

On the rare occasions where you need to reach deeply into a structure built of nested sequences, destructuring often still produces readable code but also writing it out longhand is no great burden. It's also a good hint to you that maybe you should abstract thing a bit more rather than working with so many layers of primitive combinators directly.

Source https://stackoverflow.com/questions/65969462

QUESTION

How can I use conditionals in python to solve the code shown below?

Asked 2020-Jun-08 at 18:36

My intention is to create a user dictionary that contains 'username', 'password' and 'age' and to use conditions to test if an object outside what is in the dictionary will be accepted, just like a login page on a site. But I didn't get my desired result because of an error I made. What do I need to do to make the conditionals produce my desired results? And since dictionaries are mutable, what can I do to ensure the username and password are immutable?

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ANSWER

Answered 2020-Jun-08 at 16:21

I guess you're asking about the ternary operator

Syntax :

Source https://stackoverflow.com/questions/62266262

QUESTION

Adding data to a Dict

Asked 2017-May-25 at 21:13

So, I'm trying to build a Flask app that keep track off my TV shows (just doing for fun)... but right now I'm trying to deal with the API itself (TVmaze), I'm gonna use "Arrow" as an example. What I want to do is create a dict like this all_seasons = {season_number:{'ep_number':{'ep_name':'Exemple...', ep_num: ep_number}}} so for example if I want to get the name of the season 4 22th episode I would do like this all_seasons[4][22]['ep_name'] and somehow I manage to do that (sort of), but that is what I'm getting:

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ANSWER

Answered 2017-May-25 at 21:13

You are replacing the dictionaries on each iteration instead of adding the new data. Try something like this:

Source https://stackoverflow.com/questions/44174831

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

Vulnerabilities

No vulnerabilities reported

Install SCHISM

You can download it from GitHub.
You can use SCHISM 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.