magi | web application from the Raphael Lab

by raphael-group JavaScript Version: v0.0.4 License: MIT

X-Ray Key Features Code Snippets Community Discussions(9)Vulnerabilities Install Support

kandi X-RAY | magi Summary

magi is a JavaScript library. magi has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

MAGI is a platform for interactive visualization and collaborative annotation of combinations of genetic aberrations. MAGI allows users to upload their own private datasets and view and annotate them in combination with public datasets. This repository contains the source code for MAGI. MAGI is written in Node.js with a MongoDB database. MAGI uses D3, jQuery, and GD3 on the front-end. Below, we describe how to get a version of MAGI running on your personal machine.

Support

Quality

Security

License

Reuse

Support

magi has a low active ecosystem.

It has 20 star(s) with 7 fork(s). There are 11 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 5 have been closed. On average issues are closed in 264 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of magi is v0.0.4

Quality

magi has 0 bugs and 0 code smells.

Security

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

magi code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

magi is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

magi releases are available to install and integrate.

Installation instructions are available. Examples and code snippets are not available.

Top functions reviewed by kandi - BETA

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

load data and mutation of a dataset
Create a new mutation
Completely load dataset data
Initialize the session
chart for the mutation
Initializes the query widget .
Draws the transcript panel
Update the colors
Compute summary for the mutation
Draw ARA and RGBA

Get all kandi verified functions for this library.

magi Key Features

No Key Features are available at this moment for magi.

magi Examples and Code Snippets

No Code Snippets are available at this moment for magi.

Community Discussions

Trending Discussions on magi

Altering facet_grid() height only for one facet (row) is it possible?

return union type Promise not working

Extract text from each line from a multiple-line text file based on a condition, Linux

how to discard a random number after it has been used?

Pyinstaller: trying to exclude all modules in subfolder, but pyinstaller keeps compiling them in anyway

Problem with the 0th harmonic of the Power Spectrum of an array

Struggling to get model + observable + firebase to work

no text tag(i.e.

Want to detect blur from image, but couldn't get it right

QUESTION

Altering facet_grid() height only for one facet (row) is it possible?

Asked 2022-Mar-19 at 09:18

I'm trying to improve a simple but important detail in my facet_grid graphic.

I played with scale and space parameteres of facet_grid() function. But I would like to increase the height only for the bottom facet in order to be possible to read the sample count that appears cut off in the graph (highlighted in red). See Image1. The code used is:

...

ANSWER

Answered 2022-Mar-18 at 15:47

Grid graphics enable you to modify the widths and heights of ggplot() objects.

Sample code:

Source https://stackoverflow.com/questions/71528148

QUESTION

return union type Promise not working

Asked 2022-Jan-12 at 18:48

I am trying to make a function return two possible types of data. The first type one it could return is of string the second type it could return is of fs.WriteStream

In the function this is based on a parameter you pass to it called stream?: boolean

As you can see in the picture, VSCode correctly shows this behaviour of this function

However, somehow the intellisense recognizes it only as it being a string while the actual type could also be of fs.WriteStream

But if I force it to be of type fs.WriteSteam using

...

ANSWER

Answered 2022-Jan-12 at 18:34

Why you get this error:

The type of the tt variable is string | fs.WriteStream. Since you don't know which of the two types you have in that variable, any method or property that you want to access has to be present on both types.

As you saw, you can fix that by narrowing the variable's type to just one side or the other of that union. You can do that with a manual cast (your as fs.WriteStream) or TypeScript can infer the correct type if you use control flow to check:

Source https://stackoverflow.com/questions/70686545

QUESTION

Extract text from each line from a multiple-line text file based on a condition, Linux

Asked 2021-Nov-17 at 12:55

I have a txt file with only one column that each line represent a different fastq.gz file from a sequence output. See an example below:

...

ANSWER

Answered 2021-Nov-17 at 12:55

1st solution: To get your shown expected sample output you need not to first substitute - to - and then print, we can use power of awk here to create multiple field separators and then print needed value accordingly.

Source https://stackoverflow.com/questions/70004032

QUESTION

how to discard a random number after it has been used?

Asked 2021-Oct-30 at 20:03

I am programming a program to test my chemistry knowledge. But I want once a random number appears, it won't appear a second time. For example, when the number 1 appears (hydrogen), it will not appear twice. How to do it? ---the programming language i am using is python--- My English is not good, so there is a grammar mistake, please forgive me THANKS FOR THE HELP

...

ANSWER

Answered 2021-Oct-30 at 13:52

To randomize the order in which the questions appear, you can generate a random list of unique integers in a range that will correspond to your question numbers.

First, create an empty list. Create a loop that generates a random number as long as the list length is less than your total number of questions. On each iteration, check if the random number is in the list. If it isn't append it to the list. Then, use these values to randomize your question numbers:

Source https://stackoverflow.com/questions/69780005

QUESTION

Pyinstaller: trying to exclude all modules in subfolder, but pyinstaller keeps compiling them in anyway

Asked 2021-Aug-31 at 11:40

I'm currently attempting to implement a card game in python, and my plan was to try to be user-friendly by compiling the main application to not require the user having a python installation, but to also support user modifications in a reasonably-accessible way by allowing the compiled application to load non-compiled python files from specific subfolders. This is so far working fine in the non-compiled application.

However, I can't get pyinstaller to stop including the python files that need to be separate from the compiled application.

Files:

...

ANSWER

Answered 2021-Aug-31 at 11:40

Ultimately, what I had to do to get it working was:

Move the entire data folder to a separate project, stopping pyinstaller from picking it up. Pyinstaller only has access to main.py and gameobj.py.
Change how main.py looks for imports:

Source https://stackoverflow.com/questions/68974595

QUESTION

Problem with the 0th harmonic of the Power Spectrum of an array

Asked 2021-Aug-27 at 17:17

this is my first question! The problem I'm trying to solve is: I'm creating a fingerprint pattern recognition program using OpenCV in C++. Following the paper I'm studying, I'm stuck on this part where it's said:

Compute the X-Signature array of values -> xSig[0, ..., w-1] (I've already done this part)
Compute the Power Spectrum, P[k], of the X-Signature where k=0 is the 0th harmonic and so on...

Now: the power spectrum I calculated is made by

...

ANSWER

Answered 2021-Aug-27 at 16:08

abs is the wrong operation. You need split followed by magnitude to get the norm of the packed complex numbers you got from dft.

Also your input vector may be far too short if you don't get any higher order harmonics.

Source https://stackoverflow.com/questions/68956136

QUESTION

Struggling to get model + observable + firebase to work

Asked 2021-Aug-18 at 20:56

I have a data model that looks something like this (summary, not the full thing):

...

ANSWER

Answered 2021-Aug-18 at 20:56

From looking at your code, you’ve subscribed to the call and inside your saying you want this.magus to equal your object magi but this.magus is a type of observable, so you need to say this.magus = Observable.of(magi)

Long story short you need to ensure this.magus is assigned a type observable of Magus

Source https://stackoverflow.com/questions/68839063

QUESTION

no text tag(i.e.

Asked 2020-Jul-18 at 16:08

my html is -

...

ANSWER

Answered 2020-Jul-12 at 14:50

you have to change your h1 styles:

Source https://stackoverflow.com/questions/62861829

QUESTION

Want to detect blur from image, but couldn't get it right

Asked 2020-Jun-29 at 12:43

I am actually want to convert this blur detection into C++. As a beginner in OpenCV, I am actually following this for conversion, But maybe I am getting it wrong. Here is my approach. I have to use DFT instead of FFT in C++.

...

ANSWER

Answered 2020-Jun-29 at 12:43

I think this comes close to the original Python code

Source https://stackoverflow.com/questions/62611751

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

Vulnerabilities

No vulnerabilities reported

Install magi

Setup consists of five basic steps:. Set the following environment variables to customize MAGI. To use authentication with MAGI, you will need to obtain Google OAuth2 credentials and set the appropriate environment variables. Similarly, to use the MAGI feedback tool you will need to obtain a WebEngage ID. If you want to be a webmaster for your version of MAGI on Google and Bing, you will need MAGI to serve XML files. Google and Bing will provide the XML files and specific paths/names, which you can set with the following variables. MAGI can retrieve protein-protein interactions and mutation annotations from a MAGI annotations Postgres database. To do so, set the following environment variables. We provide a tarball of data used in MAGI (currently ~100Mb) on the Raphael group website. This includes general datasets -- HG19 gene locations, cancer acronyms and descriptions, known gene sets from KEGG and PINdb -- and also mutation datasets.
Install Node, Python, and MongoDB (as described above).
Create an ENVIRONMENT file with your settings, with one export VARIABLE_NAME="..." per line. Make sure to load the environment variables into whatever shell you are running. We provide more information below.
Run (possibly a subset of the ) commands in setup.sh to install dependencies, download data, and initialize the database. We provide more information below.
Start the server with node server, which serves to http://localhost:8000 by default.

Support

MAGI was created and is maintained by the Raphael research group in the Center for Computational Molecular Biology and the Department of Computer Science at Brown University. We offer support for MAGI on the MAGI Google Group, or please visit the group website to contact us.

Find more information at: