Clair | using deep neural network on pileup data | Genomics library

by HKU-BAL Python Version: v2.1.1 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | Clair Summary

Clair is a Python library typically used in Artificial Intelligence, Genomics applications. Clair has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However Clair build file is not available. You can download it from GitHub.

Clair3 released in May 2021 is the successor of Clair, please try out Clair3 at Single-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling, complex genome assembly, and epigenetic mark detection. However, the lack of a highly accurate small variant caller has limited the new technologies from being more widely used. In this study, we present Clair, the successor to Clairvoyante, a program for fast and accurate germline small variant calling, using single molecule sequencing data. For ONT data, Clair achieves the best precision, recall and speed as compared to several competing programs, including Clairvoyante, Longshot and Medaka. Through studying the missed variants and benchmarking intentionally overfitted models, we found that Clair may be approaching the limit of possible accuracy for germline small variant calling using pileup data and deep neural networks. This is the formal release of Clair (Clair v2, Dec 2019). You can find the experimental Clair v1 (Jan 2019) at The preprint of Clair v2 is available in bioRxiv.

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Support

Clair has a low active ecosystem.

It has 96 star(s) with 12 fork(s). There are 6 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 51 have been closed. On average issues are closed in 73 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of Clair is v2.1.1

Quality

Clair has 0 bugs and 0 code smells.

Security

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

Clair code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Clair 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

Clair releases are available to install and integrate.

Clair has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Build the graph
Creates an adaptive LSTM layer
Returns a list of all available GPUs
Compute the focal loss between target and target_tensor
Make candidates
Get the reference sequence from a FASTA file
Checks if there are soft clipped bases for a given CIGAR
Given a dictionary of variants and a set of variants find those that are near the same range
Output a variant
Load the model
Export binary model to binary file
Evaluate a model
Load data from a binary file
Calculate batch output for a mini - batch
Parse command line arguments
Check the return code
Load data from a directory
Given a list of variants that have the same quality score
Parse a single variant from a single column
Create PNG file
Generate tensors from a given file
Validate and return a dictionary of inputs
Perform batch prediction
Main function
Train the model
Outputs an AlnTensor object

Get all kandi verified functions for this library.

Clair Key Features

No Key Features are available at this moment for Clair.

Clair Examples and Code Snippets

No Code Snippets are available at this moment for Clair.

Community Discussions

Trending Discussions on Clair

Is there an R function to help turn State abbreviations into full names? Or Vice Versa?

Powershell process single array in foreach loop versus multi aray in foreach loop

Promise.race() multiple resolved promises

Create new column using str.contains and based on if-else condition

Splitting addresses using the space after the postal code with regex Java

Take in values from CSV to use in a function

Conversion of data type in R does not seem to work as expected

Excel - Extracting substring after a character contained in a string

how to grid panel plots such that they have categorical variables and different x variables in ggplot in R

Not able to match same json which has mismatch in indexes of array of objects (Karate)

QUESTION

Is there an R function to help turn State abbreviations into full names? Or Vice Versa?

Asked 2022-Apr-18 at 03:52

I have two large-ish data frames I am trying to append...

In df1, I have state codes, county codes, state names (Alabama, Alaska, etc.), county names, and years from 2010:2020.

In df2, I have county names, state abbreviations (AL, AK), and data for the year 2010 (which I am trying to merge into df1. The issue lies in that without specifying the state name and simply merging df1 and df2, some of the data which I am trying to get into df1 is duplicated due to there being some counties with the same name...hence, I am trying to also join by state to prevent this, but I have state abbreviations, and state names.

Is there any way in which I can make either the state names in df1 abbreviations, or the state names in df2 full names? Please let me know! Thank you for the help.

Edit: dput(df2)

...

ANSWER

Answered 2022-Apr-18 at 03:52

Here's one way you could turn state abbreviations into state names using R's built in state vectors:

Source https://stackoverflow.com/questions/71907258

QUESTION

Powershell process single array in foreach loop versus multi aray in foreach loop

Asked 2022-Mar-27 at 03:46

i have 3 arrays with 3 elements in each array

when i run it in foreach loop it works just fine and produces desired results

...

ANSWER

Answered 2022-Mar-27 at 03:46

The reason why PowerShell does this is because on your second example, $All_OUs is an array while on your first example, $All_OUs is an array of arrays.

You could force $All_OUs to be an array of arrays by adding the Comma operator ,:

Source https://stackoverflow.com/questions/71632779

QUESTION

Promise.race() multiple resolved promises

Asked 2022-Jan-12 at 11:25

The Promise.race() method returns a promise that fulfills or rejects as soon as one of the promises in an iterable fulfills or rejects, with the value or reason from that promise.

Taken from MDN site.

I have 5 promises and I need to know once any 2 promises are resolved, taking performance under consideration.

...

ANSWER

Answered 2021-Dec-20 at 17:06

You could write a custom implementation of Promise.race that returns a promise that is resolved with the result of 2 promises that are resolved before others.

Following code example shows an implementation:

Source https://stackoverflow.com/questions/70420820

QUESTION

Create new column using str.contains and based on if-else condition

Asked 2022-Jan-04 at 13:41

I have a list of names 'pattern' that I wish to match with strings in column 'url_text'. If there is a match i.e. True the name should be printed in a new column 'pol_names_block' and if False leave the row empty.

...

ANSWER

Answered 2022-Jan-04 at 13:36

From this toy Dataframe :

Source https://stackoverflow.com/questions/70579291

QUESTION

Splitting addresses using the space after the postal code with regex Java

Asked 2021-Dec-24 at 18:03

There are some raw rows with two or more addresses, I want to split them based on the last part of the Canadian postal code using a look-arround mechanism. The Canadian postal code format is A1A 1A1, where A is a letter and 1 is a digit, with a space separating the third and fourth characters.

Here is an example

160 Rue, Notre Dame N, Bureau 140, Sainte-Marie, G6E 3Z9 887 Chemin du Bord de l'Eau, Saint-Henri de Levis, G0R 3E0

I want to split the address based on the space after the last part of postal code if it exists The result:

...

ANSWER

Answered 2021-Dec-24 at 18:03

You can use

Source https://stackoverflow.com/questions/70475069

QUESTION

Take in values from CSV to use in a function

Asked 2021-Dec-07 at 10:23

I have written a function that takes in the normal force, mass, acceleration, and coefficient of friction and calculates the applied force. I have the values of the parameter for which I need the applied force to be calculated. How do I take in the value from CSV and calculate the applied force. I have tried many times but could not figure it out. Here's my code:

...

ANSWER

Answered 2021-Dec-07 at 09:18

You can try using pandas, a well-known library for data processing.

Sample code:

Source https://stackoverflow.com/questions/70257197

QUESTION

Conversion of data type in R does not seem to work as expected

Asked 2021-Nov-16 at 05:57

I could really use some help here with my RStudio.

I am trying out this analysis and seem to have problem converting data type of certain variables.

...

ANSWER

Answered 2021-Nov-16 at 05:57

You can also specify the variable type when the data is read using read_csv.

Something like this:

Source https://stackoverflow.com/questions/69984070

QUESTION

Excel - Extracting substring after a character contained in a string

Asked 2021-Nov-03 at 21:39

I am trying to extract partial string contained within a cell after a certain character in the string.

I have a formula which can do this

...

ANSWER

Answered 2021-Aug-25 at 19:11

You could use:

Source https://stackoverflow.com/questions/68928605

QUESTION

how to grid panel plots such that they have categorical variables and different x variables in ggplot in R

Asked 2021-Oct-15 at 07:06

My actual data is something like data below. My code is producing two separate plots like two top ones in the pic below. but I want them to be in one single plot, like the bottom plot in the pic.

...

ANSWER

Answered 2021-Oct-15 at 07:06

I hope this is your want

Source https://stackoverflow.com/questions/69575782

QUESTION

Not able to match same json which has mismatch in indexes of array of objects (Karate)

Asked 2021-Oct-12 at 13:07

Trying to match two jsons, but getting test fails. Well, both jsons are the same but objects indexes inside the array are not same. I think should not make any difference. Following are two jsons: This is the code line: And match response contains ScenarioModelResponse where **response : **

...

ANSWER

Answered 2021-Oct-12 at 13:07

The arrays are NOT the same. This can be solved in 2 lines:

Source https://stackoverflow.com/questions/69540993

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

Vulnerabilities

No vulnerabilities reported

Install Clair

Then download the trained models referring to download the trained model in Installation - Option 1.
To check the version of Tensorflow you have installed:.
Each model has three files model.data-00000-of-00001, model.index, model.meta. Please give the MODEL variable, the prefix model.

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 .

Find more information at: