clipper | A tool to identify CLIP-seq peaks | Machine Learning library

by YeoLab Python Version: 0.2.0 License: Non-SPDX

X-Ray Key Features Code Snippets(3)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | clipper Summary

clipper is a Python library typically used in Artificial Intelligence, Machine Learning, Tensorflow applications. clipper has no bugs, it has no vulnerabilities, it has build file available and it has high support. However clipper has a Non-SPDX License. You can install using 'pip install clipper' or download it from GitHub, PyPI.

A tool to detect CLIP-seq peaks. Please visit our wiki page to learn more about usage of clipper:

Support

Quality

Security

License

Reuse

Support

clipper has a highly active ecosystem.

It has 54 star(s) with 39 fork(s). There are 38 watchers for this library.

It had no major release in the last 12 months.

There are 46 open issues and 58 have been closed. On average issues are closed in 572 days. There are 1 open pull requests and 0 closed requests.

It has a positive sentiment in the developer community.

The latest version of clipper is 0.2.0

Quality

clipper has no bugs reported.

Security

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

License

clipper 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

clipper 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.

Top functions reviewed by kandi - BETA

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

Main entry point for the script
Run call_peaks on each gene
Calculate peak definitions
Get all reads in a pysam
Build transcript data
Build a dictionary of gene lengths
Build a dictionary of gene information
Get a set of accepted species
Return an option parser
Get FDR cutoff mode
Returns the peaks in the model
Plot the curve
Override parser options
Return a poisson P
Calculate the Poisson P
Create a poisson P
Return path to data file
Returns the directory containing the data directory
Return path to test directory
Returns the path to test files

Get all kandi verified functions for this library.

clipper Key Features

No Key Features are available at this moment for clipper.

clipper Examples and Code Snippets

CLIPper - CLIP peak enrichment recognition,Installation

Python

Lines of Code : 5

License : Permissive (MIT)

Copy

# recreate PYTHON3 conda environment
cd clipper
conda env create -f environment3.yml
conda activate clipper3
pip install .

CLIPper - CLIP peak enrichment recognition,Command Line Usage

Python

Lines of Code : 5

License : Permissive (MIT)

Copy

# shows all the options
clipper -h 

# minimal command
clipper -b YOUR_BAM_FILE.bam -o YOUR_OUT_FILE.bed -s hg19

CLIPper - CLIP peak enrichment recognition,Run test

Python

Lines of Code : 2

License : Permissive (MIT)

Copy

cd clipper/clipper/test
python -m unittest discover

Community Discussions

Trending Discussions on clipper

Function is running twice but only being called once?

Flutter: Can't make a ClipPath

Why is this boxshadow not appearing?

flutter: Change path shape position in grid view items

Graphing Multiple Variables Using Python and Seaborn/Pandas

Cannot map protocol compliant elements to generic elements

Decoding an array of objects with nested heterogeneous child objects

How to get rid of line between appbar and body?

Bottom Overflowed by 81 Pixels

flutter: custom shape as text background

QUESTION

Function is running twice but only being called once?

Asked 2021-May-31 at 22:44

This code works. It throws an error on the first getClipFile, because ffmpeg hasn't completed. I kind of understand that, but also it's running again somehow?

I want to make it run once, after the my bash script has completed. I also cannot understand how to simply wrap it all in a function and just wait on it.

Thanks! The JS:

...

ANSWER

Answered 2021-May-31 at 21:55

You need to wait for the end event before calling getClipFile(). You're calling it every time you get a buffer of data.

Source https://stackoverflow.com/questions/67780526

QUESTION

Flutter: Can't make a ClipPath

Asked 2021-May-31 at 16:44

Can someone help me with this ClipPath in Flutter?

I can't make the bottom border.

Also, how can I make it visible as a Row child?

I noticed that it works in Container, but it doesn't in when I drag the Container(or Flexible) in Row or without the widgets.

UPDATE

This is the return when the ClipPath is not visible

...

ANSWER

Answered 2021-May-31 at 16:44

Use your AuthClipPath() like this inside Row()

Source https://stackoverflow.com/questions/67774022

QUESTION

Why is this boxshadow not appearing?

Asked 2021-May-10 at 03:24

I'm working on a little widget and for some reason I cannot get the boxshadow to appear. I've set it on the container and I have no idea why it isn't working. I'm guessing it has something to do with ClipPath?

...

ANSWER

Answered 2021-May-09 at 17:40

Put ClipPath widget in a Material widget and give it an elevation like this:

Source https://stackoverflow.com/questions/67460363

QUESTION

flutter: Change path shape position in grid view items

Asked 2021-May-02 at 12:27

In my page I have a gridview. In gridview items I use ClipPath. The problem is here. The path that I shows is on top and it is not possible to change it's position into the bottom:

...

ANSWER

Answered 2021-May-02 at 12:27

here is my result, I think so the problem is in the ChartDegreeArtWidget, use the code below

Source https://stackoverflow.com/questions/67354093

QUESTION

Graphing Multiple Variables Using Python and Seaborn/Pandas

Asked 2021-Apr-30 at 04:19

I want to create a graph that combines these three variables. I want to do this so I can see if the team's average win rating has an effect on the home crowd attendance. I have attached an image of what my data frame looks like. I am open to multiple graphs and would love to look at multiple different solutions for this if possible!

Here is an example code to get you started. nba = pd.DataFrame([['Spurs', 18459.4, .741800], ['Thunder', 18203.0, 676800], ['Clippers', 19203.4, .662600], ['Warriors', 19403.6, .650000]], columns = ['Team', 'Home: Avg Attendance', 'Winning Percentage'])

...

ANSWER

Answered 2021-Apr-30 at 04:19

The graph function of panndas allows you to create a composite graph with the number of spectators and the winning percentage. This is the simplest example.

Source https://stackoverflow.com/questions/67327688

QUESTION

Cannot map protocol compliant elements to generic elements

Asked 2021-Apr-23 at 15:05

As you can see below, I downloaded an array of structures containing heterogeneous objects that were decoded into enums containing nested objects.

I would now like to put said objects into a generic Model structure, but the compiler won't allow this - the error is described below in the code comment. I am relatively new to programming in Swift, I would appreciate your help.

...

ANSWER

Answered 2021-Apr-23 at 15:05

You do not need generics here.

Change Model to accept any type that conforms to Displayable in the init

Source https://stackoverflow.com/questions/67228972

QUESTION

Decoding an array of objects with nested heterogeneous child objects

Asked 2021-Apr-22 at 17:36

An example of the response from the server is below.

The list consists of elements that have heterogeneous substructures in the info fields. Each of them contains 3 fields with the same types, but they have different keys.

I don't know how to decode this, I haven't encountered such a problem so far. I can't find an example on the Internet that fits this case.

I wanted to decode the enum type at the beginning and select the appropriate info structure based on it, but it doesn't work.

I would very much appreciate your help.

...

ANSWER

Answered 2021-Apr-22 at 17:36

Your code on pastebin is too complicated, I mean this

Source https://stackoverflow.com/questions/67216987

QUESTION

How to get rid of line between appbar and body?

Asked 2021-Apr-06 at 07:53

I have an appbar and in the body I have a column. I want to make it in such a way that you do not realise where the appbar ends and the column begins. For that, I've set the elevation of the appbar to zero and the background color of both the appbar and the widget in the column to be the same. Yet, there seems to be a line that divides the two that I just can't get rid of.

Here's the code:

...

ANSWER

Answered 2021-Apr-06 at 07:53

give your scaffold a background color the same as your appBar color. In my pictures, the color is orange.200 and I get those images, in your case, use blue as the code.

Source https://stackoverflow.com/questions/66964260

QUESTION

Bottom Overflowed by 81 Pixels

Asked 2021-Mar-25 at 03:46

I'm pretty much self-tutoring flutter and I'm working on a personal project. I wrapped it to singlechildscrollview but it still produces the problem. The code below:

...

ANSWER

Answered 2021-Mar-19 at 13:01

Wrap the SingleChildScrollView in Expanded Widget.

You can make use of the flutter dev tools for identifying overlapping issues.

Source https://stackoverflow.com/questions/66706063

QUESTION

flutter: custom shape as text background

Asked 2021-Mar-22 at 13:09

I need to achieve this in flutter:

I tried making a Row and setting a background to the Text to handle the ractangle, then a ClipPath to make the triangle. The problem with this is that the edge is not precise (you can see a thin line between the rectangle and the triangle in the image below), also the ClipPath has fixed size so if I want to change the text size at some point I'll have to fine-tune the triangle again.

here's my code:

...

ANSWER

Answered 2021-Mar-22 at 12:45

You can try the following code:

Source https://stackoverflow.com/questions/66745841

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

Vulnerabilities

No vulnerabilities reported

Install clipper

Thanks @rekado for making clipper available at GNU Guix guix install clipper
We notice installation might be failing in some platform. Dockerized clipper is in the eclip repository here.

Support

How do use additional reference genome? See here for instructions: Supporting additional species. Where can I use specify the Input bam file? Currently CLIPper does include input normalization. The input normalization pipeline is in another repository: Merge Peaks.

Find more information at: