Skyhawk | Artificial Neural Network-based discriminator | Genomics library

by aquaskyline Python Version: Current License: Non-SPDX

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

kandi X-RAY | Skyhawk Summary

Skyhawk is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. Skyhawk has no bugs, it has no vulnerabilities and it has low support. However Skyhawk build file is not available and it has a Non-SPDX License. You can download it from GitHub.

With the increasing throughput and reliability of sequencing technologies in the recent years, it is getting common that medical doctors rely on sequencing to make better diagnostics for cancers and rare diseases. Among the interpretable results that sequencing can provide, genetic variants that have been reported in renowned databases such as Clinvar and HGMD, with evidence showing that they associate with certain symptoms and therapies, are considered as actionable genetic variant candidates. However, even though the state-of-the-art variant callers achieve better precision and sensitivity, it is still not uncommon for the variant callers to produce false positive variants with somehow a pretty high probability, which makes them unable to tell apart from the true positives. The situation gets even worse when the callers are set to favor sensitivity over precision, which is often the case in clinical practices. The false positives variants, if not being sanitized, will lead to a spurious clinical diagnosis. Instead of relying only on what a variant caller tells, clinical doctors usually verify the correctness of actionable genetic variants by eyes, with the help of IGV or SAMtools tview. 'Skyhawk' was designed to expedite the process and save the doctors from eye checking the variant, using a deep neural network based "eye", trained with millions of samples on how a true variant "looks like" in different settings.

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Quality

Security

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Support

Skyhawk has a low active ecosystem.

It has 32 star(s) with 5 fork(s). There are 2 watchers for this library.

It had no major release in the last 6 months.

There are 1 open issues and 9 have been closed. On average issues are closed in 24 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Skyhawk is current.

Quality

Skyhawk has 0 bugs and 0 code smells.

Security

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

Skyhawk code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Skyhawk 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

Skyhawk releases are not available. You will need to build from source code and install.

Skyhawk 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.

Skyhawk saves you 571 person hours of effort in developing the same functionality from scratch.

It has 1334 lines of code, 55 functions and 11 files.

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

Top functions reviewed by kandi - BETA

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

Run check
Get a tensor
Runs the model without training
Checks if a command exists
Setup environment variables
Restore parameters from a function
Checks if file exists
Close the session
Unpack an ATTRAN record
Outputs an AlnTensor
Generates Tensor
Generator for reading reads
Yield candidates from start to end
Build the graph
Wrapper for dropout
Build a training array from a TensorBoard
Output a variant
Annotate a VCF file with annotations
Check and exit code
Tries to poll the server

Get all kandi verified functions for this library.

Skyhawk Key Features

No Key Features are available at this moment for Skyhawk.

Skyhawk Examples and Code Snippets

No Code Snippets are available at this moment for Skyhawk.

Community Discussions

Trending Discussions on Skyhawk

How to load XML data to a data structure?

Grouping Tables in Python

Return multiple XML nodes and Custom parent tag using FLWOR XQuery

Count the No of Occurrences of a word in xml using c#

How to parse an XML element root an select some values of it in Java?

Content over footer

Universal NavBar Links

Half of CSS Not Being Displayed

Encircle points with shaded blobs

Pipe-lining / keyby of keyby of an RDD in pyspark(spark)

QUESTION

How to load XML data to a data structure?

Asked 2021-Jan-23 at 07:55

I have the following XML document

...

ANSWER

Answered 2021-Jan-23 at 07:55

I know this is not quite in the spirit of the question. However, it should be as simple as

Source https://stackoverflow.com/questions/65856219

QUESTION

Grouping Tables in Python

Asked 2020-Apr-19 at 17:41

I have a table that looks like this -

...

ANSWER

Answered 2020-Apr-19 at 17:41

If you want the Manufacturer to be sorted by the amount of Models:

Source https://stackoverflow.com/questions/61306662

QUESTION

Return multiple XML nodes and Custom parent tag using FLWOR XQuery

Asked 2019-Jun-28 at 08:44

I need to get the following output using a FLWOR expression.

...

ANSWER

Answered 2019-Jun-28 at 08:44

You only want to create one oldPlanes element so its construction needs to be outside the FLWOR expression:

Source https://stackoverflow.com/questions/56802601

QUESTION

Count the No of Occurrences of a word in xml using c#

Asked 2018-Nov-23 at 14:29

I have an XML file in which I have to find the number of occurrences of a word i the XML file. Consider, I have a sample XML file as below

...

ANSWER

Answered 2018-Nov-23 at 08:41

Based on what you've asked for, Regex.Matches(File.ReadAllText(myFile), "Gold").Count will do the job, probably more efficiently than anything you can write yourself. But a more interesting problem is to find all planes whose Color property is Gold :)

(oh I forgot to ask about case sensitivity, but you can specify that in the 2nd parameter to Regex.Matches)

Source https://stackoverflow.com/questions/53443005

QUESTION

How to parse an XML element root an select some values of it in Java?

Asked 2018-Oct-16 at 11:28

I am looking for a practical way to parse an xml root element an get some values from it. I have tried many ways, but none of them are efficient.

...

ANSWER

Answered 2018-Oct-15 at 19:19

Try with marshaling and unmarshalling mechanism

Source https://stackoverflow.com/questions/52823324

QUESTION

Content over footer

Asked 2018-Sep-18 at 16:00

So I have reviewed all of the posts about this and have tried everything... My content is pushing my footer down as I want. However, there is a very small portion of a div that is overlaying my footer. It can be found at http://www. newshongumpto.org

Its only that bottom portion of the div and I cannot figure out why. I had to move my footer css to the actual includes files as it wasn't find the media query to hide the footer on mobile but I digress. I know, a lot going on here:

Site CSS:

...

ANSWER

Answered 2018-Sep-18 at 16:00

You have this...

Source https://stackoverflow.com/questions/52390492

QUESTION

Universal NavBar Links

Asked 2018-Sep-14 at 13:12

So I get that that is a silly beginner question, but I can't figure it out. Its two parts:

THE SETUP
So I want to have a universal navbar on my site. I created a navigation.php file and I am using include on every page.

THE PROBLEM
On my index page, it is working great. However all of my other pages are within a contentFiles folder. When I navigate from the index page, back to the index page the contentPages, the sub-directory stays in the URL.

To see exactly what it is doing: 1. Go to http://www.newshongumpto.org 2. Click on News/Calendar > Calendar 3. Click on Home

Any suggestions? My next questions is how to make this dynamic from my dB, but I think I will attempt that first before coming back.

...

ANSWER

Answered 2018-Sep-14 at 12:58

Change href="index.php" to href="/index.php"

Similarly add slash to all your urls . This way, all your urls will be routed from your website's base url

Source https://stackoverflow.com/questions/52332436

QUESTION

Half of CSS Not Being Displayed

Asked 2018-Aug-23 at 00:38

I'm so done looking at this code. I simply cannot find where I am making a mistake, however only a portion of my CSS is processing for my page. Literally, from the image down, and yet I am unable to find any issue. Even the gradient is processing correctly. Ironically, the footer, for example, is in fact processing here. Any ideas?

...

ANSWER

Answered 2018-Aug-23 at 00:38

I believe the problem is simply too many errors in your CSS. It is not that part of your stylesheet is not being applied, it is that many of your rules are written incorrectly so that they do not style elements as you appear to intend. For example, this selector

Source https://stackoverflow.com/questions/51976768

QUESTION

Encircle points with shaded blobs

Asked 2018-Mar-02 at 16:10

So I would like to make a plot that would have my points for 3 different groups (cars) but as a general area , much like the blobs on this sketch. Ideally it would have a darker hue in the areas where the points lay. Any ideas?

DATA TO WORK WITH

...

ANSWER

Answered 2018-Mar-02 at 16:09

You can use function geom_encircle from package ggalt to draw "blobs" (decrease alpha for shaded area).

Source https://stackoverflow.com/questions/49071628

QUESTION

Pipe-lining / keyby of keyby of an RDD in pyspark(spark)

Asked 2017-Apr-01 at 12:16

I have an rdd as rowsrdd given below, to which i have apply aggregation by using keyby() on keys (0,8) and reducebykey() on key (1):

...

ANSWER

Answered 2017-Apr-01 at 12:16

You should map country_name as your sole key, and then you can just use reduceByKey():

Source https://stackoverflow.com/questions/43156082

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

Vulnerabilities

No vulnerabilities reported

Install Skyhawk

Please refer to the Clairvoyante project.

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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