Clinotator | Clinical interpretation of ambiguous ClinVar annotations | Data Labeling library

by rbutleriii Python Version: v1.4.0 License: GPL-3.0

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

kandi X-RAY | Clinotator Summary

Clinotator is a Python library typically used in Artificial Intelligence, Data Labeling applications. Clinotator 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 download it from GitHub.

Clinical interpretation of ambiguous ClinVar annotations

Support

Quality

Security

License

Reuse

Support

Clinotator has a low active ecosystem.

It has 6 star(s) with 0 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 3 have been closed. On average issues are closed in 5 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Clinotator is v1.4.0

Quality

Clinotator has no bugs reported.

Security

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

License

Clinotator 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

Clinotator releases are available to install and integrate.

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

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Parse input file into NCBI XML
Try to connect to NCBI
Parses a VCF file into a list of dictionaries
Download XML files from NCBI
Perform a batch of query results
Parse the assertion table
Parses the assertion
Return weight of age
Calculate the average age of a list
Parse alleles
Return a list of haplotype terms
Calculate the CTRS score
R Determine reclassification tree
Convert variant objects to CSV format
Explode list of lists
Concatenate info column
Get CLI arguments
Set logging options
Parse query results
Parse a single VCF file into a list

Get all kandi verified functions for this library.

Clinotator Key Features

No Key Features are available at this moment for Clinotator.

Clinotator Examples and Code Snippets

Clinotator,Code Example

Python

Lines of Code : 21

License : Strong Copyleft (GPL-3.0)

Copy

usage: clinotator.py [-h] [--log] [--long-log] [-o prefix] [--version] -e
                     EMAIL -t {vid,rsid,vcf}
                     file [file ...]

Clinical interpretation of ambiguous ClinVar annotations

positional arguments:
  file

Clinotator,Installation

Python

Lines of Code : 14

License : Strong Copyleft (GPL-3.0)

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CONDA_ENV=$(conda info --base)/envs/clinotator
conda create -y -n clinotator python=3.7 biopython pandas
git clone https://github.com/rbutleriii/Clinotator.git $CONDA_ENV
ln -s $CONDA_ENV/Clinotator/clinotator/clinotator.py $CONDA_ENV/bin/clinotator.

Clinotator,Citation

Python

Lines of Code : 10

License : Strong Copyleft (GPL-3.0)

Copy

@article{key ,
	author = {Robert R Butler III and Pablo V Gejman},
	title = {Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts [version 2; referees: 2 approved]},
	journal = {F1000Research},
	volume = {7},
	year =

Community Discussions

Trending Discussions on Data Labeling

How can I do this split process in Python?

Replacing a character with a space and dividing the string into two words in R

Azure ML FileDataset registers, but cannot be accessed for Data Labeling project

QUESTION

How can I do this split process in Python?

Asked 2021-Dec-30 at 14:06

I'm trying to make a data labeling in a table, and I need to do it in such a way that, in each row, the index is repeated, however, that in each column there is another Enum class.

What I've done so far is make this representation with the same enumerator class.

A solution using the column separately as a list would also be possible. But what would be the best way to resolve this?

...

ANSWER

Answered 2021-Dec-30 at 13:57

Instead of using Enum you can use a dict mapping. You can avoid loops if you flatten your dataframe:

Source https://stackoverflow.com/questions/70532286

QUESTION

Replacing a character with a space and dividing the string into two words in R

Asked 2020-Nov-18 at 07:32

I have a dataframe that contains a column that includes strings separeted with semi-colons and it is followed by a space. But unfortunately in some of the strings there is a semi-colon that is not followed by a space.

In this case, This is what i'd like to do: If there is a space after the semi-colon we do not need a change. However if there are letters before and after the semi-colon, we should change semi-colon with space

i have this:

...

ANSWER

Answered 2020-Nov-16 at 07:24

Try something like:

Source https://stackoverflow.com/questions/64853962

QUESTION

Azure ML FileDataset registers, but cannot be accessed for Data Labeling project

Asked 2020-Oct-28 at 20:31

Objective: Generate a down-sampled FileDataset using random sampling from a larger FileDataset to be used in a Data Labeling project.

Details: I have a large FileDataset containing millions of images. Each filename contains details about the 'section' it was taken from. A section may contain thousands of images. I want to randomly select a specific number of sections and all the images associated with those sections. Then register the sample as a new dataset.

Please note that the code below is not a direct copy and paste as there are elements such as filepaths and variables that have been renamed for confidentiality reasons.

...

ANSWER

Answered 2020-Oct-27 at 22:39

Is the data behind virtual network by any chance?

Source https://stackoverflow.com/questions/64546521

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

Vulnerabilities

No vulnerabilities reported

Install Clinotator

Implemented in python (tested on 2.7.15 and >=3.5). You can git clone or download the zipfile and unpack. Add the folder location to your ~/.bash_profile or export PATH=$PATH:path/to/folder/Clinotator/clinotator.py. If you have Anaconda/Miniconda installed on your system, self contained installation can be accomplished quickly with no other modifications. The following will find your conda envs folder, create a clinotator conda environment, and install the repo in it (with a link to source the package only when the conda environment is active).

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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