MAGIC | Markov Affinity-based Graph Imputation | Genomics library

 by   KrishnaswamyLab Jupyter Notebook Version: v3.0.0 License: GPL-2.0

kandi X-RAY | MAGIC Summary

kandi X-RAY | MAGIC Summary

MAGIC is a Jupyter Notebook library typically used in Artificial Intelligence, Genomics applications. MAGIC has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data. MAGIC learns the manifold data, using the resultant graph to smooth the features and restore the structure of the data. To see how MAGIC can be applied to single-cell RNA-seq, elucidating the epithelial-to-mesenchymal transition, read our publication in Cell. MAGIC has been implemented in Python, Matlab, and R.
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            kandi-support Support

              MAGIC has a low active ecosystem.
              It has 278 star(s) with 94 fork(s). There are 22 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 24 open issues and 111 have been closed. On average issues are closed in 76 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of MAGIC is v3.0.0

            kandi-Quality Quality

              MAGIC has 0 bugs and 0 code smells.

            kandi-Security Security

              MAGIC has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              MAGIC code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              MAGIC is licensed under the GPL-2.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              MAGIC releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.
              It has 3839 lines of code, 35 functions and 10 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of MAGIC
            Get all kandi verified functions for this library.

            MAGIC Key Features

            No Key Features are available at this moment for MAGIC.

            MAGIC Examples and Code Snippets

            Generate a solution to a magic solution .
            pythondot img1Lines of Code : 31dot img1License : Permissive (MIT License)
            copy iconCopy
            def solution(gon_side: int = 5) -> int:
                """
                Find the maximum number for a "magic" gon_side-gon ring
            
                The gon_side parameter should be in the range [3, 5],
                other side numbers aren't tested
            
                >>> solution(3)
                432621513  
            Get the magic number for the magic number .
            javadot img2Lines of Code : 28dot img2no licencesLicense : No License
            copy iconCopy
            public static int getKthMagicNumber(int k) {
            		if (k < 0) {
            			return 0;
            		}
            		int val = 0;
            		Queue queue3 = new LinkedList();
            		Queue queue5 = new LinkedList();
            		Queue queue7 = new LinkedList();
            		queue3.add(1);
            		for (int i = 0; i <= k; i++)  
            Check if a ring is a magic ring .
            pythondot img3Lines of Code : 27dot img3License : Permissive (MIT License)
            copy iconCopy
            def is_magic_gon(numbers: list[int]) -> bool:
                """
                Check if the solution set is a magic n-gon ring
                Check that the first number is the smallest number on the outer ring
                Take a list, and check if the sum of each 3 numbers chunk is equ  

            Community Discussions

            QUESTION

            Signing into slack-desktop not working on 4.23.0 64-bit (Ubuntu)
            Asked 2022-Mar-22 at 21:43

            In the app, going File > Workspace > Sign in to new workspace launches a browser window. After selecting the workspace in browser, it launches back a deep link back to slack but it doesn't work. Nothing happens on the slack-desktop.

            Attempting to find out what is going on, I run the /usr/bin/slack to take a look at the logs.

            I see logs of HANDLE_DEEP_LINK but no follow up activity.

            ...

            ANSWER

            Answered 2022-Jan-26 at 16:40

            After trying various things, I noticed that what I suspect to be the workspace id, tlvs8sasf above are often in CAPS in the logs.

            So, I tried updating the deep link by upper casing the workspace id, then click on it. Voila, it worked for me. Hope this helps anyone else also suffering from this same issue.

            Source https://stackoverflow.com/questions/70867064

            QUESTION

            Where are the using statements/directives in .NET 6
            Asked 2022-Mar-15 at 17:03

            I got up and running with Visual Studio 2022 Preview for a couple of days now.

            Got the first shock, there is no Startup.cs. Thats ok, a bit of reading, I know Startup is removed.

            Today got another slap. I see no using statements. Here it is.

            I just created a brand new .NET 6 web app and as I hover over the WebApplication class, I realized it stays in Microsoft.AspNetCore.Builder namespace. And the generated Program.cs class looks like this.

            So where is the using Microsoft.AspNetCore.Builder; statement?

            Whats the magic? Why is .net becoming mystical by the day?

            The full Program.cs file is as follows.

            ...

            ANSWER

            Answered 2022-Mar-15 at 17:03

            C# 10.0 introduces a new feature called global using directive (global using ;) which allows to specify namespaces to be implicitly imported in all files in the compilation. .NET 6 RC1 has this feature enabled by default in new project templates (see enable property in your .csproj).

            For Microsoft.NET.Sdk.Web next namespaces should be implicitly imported (plus the ones from Microsoft.NET.Sdk):

            • System.Net.Http.Json
            • Microsoft.AspNetCore.Builder
            • Microsoft.AspNetCore.Hosting
            • Microsoft.AspNetCore.Http
            • Microsoft.AspNetCore.Routing
            • Microsoft.Extensions.Configuration
            • Microsoft.Extensions.DependencyInjection
            • Microsoft.Extensions.Hosting
            • Microsoft.Extensions.Logging

            UPD

            To address your questions in comment:

            At the moment of writing the generated file containing default imports will be inside the obj folder named something like ProjectName.GlobalUsings.g.cs.

            To modify default imports you can add Using element to your .csproj file. Based on exposed attributes it allows several actions including addition and removal:

            Source https://stackoverflow.com/questions/69738921

            QUESTION

            Why can't I return std::getline's as-if-boolean result?
            Asked 2022-Mar-14 at 23:01

            A standard idiom is

            ...

            ANSWER

            Answered 2022-Mar-14 at 22:53

            The boolean conversion operator for std::basic_istream is explicit. This means that instances of the type will not implicitly become a bool but can be converted to one explicitly, for instance by typing bool(infile).

            Explicit boolean conversion operators are considered for conditional statements, i.e. the expression parts of if, while etc. More info about contextual conversions here.

            However, a return statement will not consider the explicit conversion operators or constructors. So you have to explicitly convert that to a boolean for a return.

            Source https://stackoverflow.com/questions/71474982

            QUESTION

            Why do I need to touch Hash if assigned via map?
            Asked 2022-Feb-23 at 19:56

            When I do this it works (these are the last 4 lines before the end of a method TWEAK. However, my first attempt had no line #3 and failed because %!columns was empty...

            ...

            ANSWER

            Answered 2022-Feb-23 at 19:56

            Without the %!columns on line three, the call to map is lazy and thus never gets evaluated (the %!columns call wants to check the current value of columns, which implies eagerness).

            To more explicitly invoke eagerness, either use the eager statement prefix (shown below) or switch to a for loop, which is eager by default.

            I think this code will behave the way you want it to:

            Source https://stackoverflow.com/questions/71243088

            QUESTION

            Rust compiler not optimising lzcnt? (and similar functions)
            Asked 2021-Dec-26 at 01:56
            What was done:

            This follows as a result of experimenting on Compiler Explorer as to ascertain the compiler's (rustc's) behaviour when it comes to the log2()/leading_zeros() and similar functions. I came across this result with seems exceedingly both bizarre and concerning:

            Compiler Explorer link

            Code:

            ...

            ANSWER

            Answered 2021-Dec-26 at 01:56

            Old x86-64 CPUs don't support lzcnt, so rustc/llvm won't emit it by default. (They would execute it as bsr but the behavior is not identical.)

            Use -C target-feature=+lzcnt to enable it. Try.

            More generally, you may wish to use -C target-cpu=XXX to enable all the features of a specific CPU model. Use rustc --print target-cpus for a list.

            In particular, -C target-cpu=native will generate code for the CPU that rustc itself is running on, e.g. if you will run the code on the same machine where you are compiling it.

            Source https://stackoverflow.com/questions/70481312

            QUESTION

            "Could not retrieve credential from local cache for service principal" when using Azure CLI 2.30.0 credentials in Python SDK on Azure Devops MS agent
            Asked 2021-Nov-27 at 06:57

            I an Azure Pipeline on a self-hosted agent I use this task

            ...

            ANSWER

            Answered 2021-Nov-27 at 06:57

            This issue is caused by Azure CLI version 2.30.0 which seemed to be rolled out MS hosted agents recently.

            Hence I adapted all my Python scripts running on (MS and self) hosted agents to this model:

            Source https://stackoverflow.com/questions/69895247

            QUESTION

            In Blazor, is there a way to undo invalid user input, without changing the state?
            Asked 2021-Nov-26 at 19:02

            In Blazor, how can I undo invalid user input, without changing the state of the component to trigger a re-render?

            Here is a simple Blazor counter example (try it online):

            ...

            ANSWER

            Answered 2021-Nov-18 at 20:12

            Here's a modified version of your code that does what you want it to:

            Source https://stackoverflow.com/questions/70016908

            QUESTION

            How to disable Browser Link in ASP.NET Core (.NET 6, VS 2022)
            Asked 2021-Nov-14 at 03:44

            I have disabled Browser Link inside Visual Studio 2022, and I have also disabled all the Hot Reload functionality.

            Even the Browser Link Dashboard indicates it should be disabled:

            I also do not use any of the app.UseBrowserLink(); code anywhere in my code. (as documented in Browser Link in ASP.NET Core.

            However, these middlewares still somehow appear in the request pipeline:

            • Microsoft.AspNetCore.Watch.BrowserRefresh.BrowserRefreshMiddleware
            • Microsoft.WebTools.BrowserLink.Net.BrowserLinkMiddleware

            These middlewares add this to my HTML:

            ...

            ANSWER

            Answered 2021-Nov-14 at 03:44

            You are almost there. You just need to also config the following (Don't forget to restart your VS):

            Source https://stackoverflow.com/questions/69952420

            QUESTION

            Optimize the calculation of horizontal and vertical adjacency using numpy
            Asked 2021-Nov-08 at 08:55

            I have following cells:

            ...

            ANSWER

            Answered 2021-Nov-08 at 08:43

            I had a really quick attempt at this with Numba but have not checked it too thoroughly though the results seem about right:

            Source https://stackoverflow.com/questions/69854335

            QUESTION

            How to prefer calling const member function and fallback to non-const version?
            Asked 2021-Sep-21 at 05:35

            Consider a class Bar in two versions of a library:

            ...

            ANSWER

            Answered 2021-Sep-21 at 04:13

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

            Vulnerabilities

            No vulnerabilities reported

            Install MAGIC

            To install with pip, run the following from a terminal:.
            To use MAGIC, you will need to install both the R and Python packages. If python or pip are not installed, you will need to install them. We recommend Miniconda3 to install Python and pip together, or otherwise you can install pip from https://pip.pypa.io/en/stable/installing/.

            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:

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            CLONE
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            https://github.com/KrishnaswamyLab/MAGIC.git

          • CLI

            gh repo clone KrishnaswamyLab/MAGIC

          • sshUrl

            git@github.com:KrishnaswamyLab/MAGIC.git

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