MAESTRO | Single-cell Transcriptome and Regulome Analysis Pipeline | Genomics library

 by   liulab-dfci C Version: v1.5.1 License: GPL-3.0

kandi X-RAY | MAESTRO Summary

kandi X-RAY | MAESTRO Summary

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

MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis. Currently, MAESTRO support Smart-seq2, 10x-genomics, Drop-seq, SPLiT-seq for scRNA-seq protocols; microfudics-based, 10x-genomics and sci-ATAC-seq for scATAC-seq protocols.
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            kandi-support Support

              MAESTRO has a low active ecosystem.
              It has 231 star(s) with 75 fork(s). There are 12 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 24 open issues and 75 have been closed. On average issues are closed in 33 days. There are 4 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of MAESTRO is v1.5.1

            kandi-Quality Quality

              MAESTRO has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              MAESTRO is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              MAESTRO releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of MAESTRO
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            MAESTRO Key Features

            No Key Features are available at this moment for MAESTRO.

            MAESTRO Examples and Code Snippets

            No Code Snippets are available at this moment for MAESTRO.

            Community Discussions

            QUESTION

            How to I extract specific value from JSON API in PHP Laravel?
            Asked 2021-May-11 at 05:40

            I have a block of code in the controller which can make API requests and retrieve responses. So far, I only know how to print the response with the code below.

            ...

            ANSWER

            Answered 2021-May-11 at 05:25

            You can pass the result to view() function and in your blade show it.

            In your controller:

            Source https://stackoverflow.com/questions/67480966

            QUESTION

            500 Server Error in my Django App in App Engine (Google Cloud)
            Asked 2021-Mar-22 at 11:48

            I am new to Google Cloud an I followed the steps in https://cloud.google.com/python/django/appengine and deployed the App successfully. However, when I go to the page https://PROJECT_ID.REGION_ID.r.appspot.com the next message is displayed:

            Error: Server Error The server encountered an error and could not complete your request. Please try again in 30 seconds.

            I have seen this is something really usual but cannot find any useful solution. I would appreciate any help.

            my settings.py:

            ...

            ANSWER

            Answered 2021-Mar-09 at 10:44

            You have errors in your code. 500 Server Error means you have something wrong in your application.

            Source https://stackoverflow.com/questions/66545355

            QUESTION

            Laravel: Redirect with post route
            Asked 2021-Mar-08 at 00:38

            Been trying to find a way to call to pass a multidimensional array to a Post route with no success.

            The array looks like this:

            ...

            ANSWER

            Answered 2021-Mar-06 at 18:05

            It's not going to work with a simple redirection because you cannot choose the HTTP method. It's always GET when you make a redirection. It works in your test because you make a POST request manually.

            I can see 2 solutions:

            1. You can send data using GET method (they are added as URL parameters). If they are not confidential it can be a solution.
            2. If you don't want to send those data in the URL, you have to save them somewhere and get them from the storage when you're on the order.success page. You can save them, for instance, in the session storage or in the local storage of your browser.

            Also, your test isn't good if it tests a behavior that does not happen in your app (post request instead of redirection).

            Source https://stackoverflow.com/questions/66508708

            QUESTION

            TypeError: Cannot read property 'should' of undefined
            Asked 2021-Mar-04 at 17:32

            I have a function (detectNetwork) which checks a credit card number and if it matches a recognized vendor identifies the vendor for the card. I have another function (detectNetworkTest) which using Mocha can be invoked to test detectNetwork and validate it is working correctly.

            I am working on the validation for China UnionPay and receiving the following error when invoking detectNetworkTest:

            TypeError: Cannot read property 'should' of undefined at Context. (detectNetwork.test.js:241:39)

            Which refers to this line in detectNetworkTest:

            detectNetwork(cardNumberToCheck).should.equal('China UnionPay');

            When running this function I can confirm by logging to the console that cardNumberToCheck is the correct value I need to utilize so I am bit stuck on trying to determine why it is being read as undefined.

            detectNetwork

            ...

            ANSWER

            Answered 2021-Mar-04 at 17:32

            The error means detectNetwork(cardNumberToCheck) evaluates to undefined.

            This is because there is no return in case there is absolutely no match for re[card].test(cardNumber)

            Source https://stackoverflow.com/questions/66479976

            QUESTION

            Extract In-line images from Google Sheet and reinsert as links
            Asked 2021-Feb-01 at 10:06

            I have a Google sheet with approaching 100 in-line images. The sheet is very slow to load. I've read that the sheet will perform better if the images are loaded as a link from a Google Drive file rather than as an embedded image in the spreadsheet.

            So I would like to write a Google Apps Script which...

            1. looks through each cell on each worksheet;
            2. decides whether the cell contains an image;
            3. save the image to Google drive;
            4. get a link to the image file;
            5. delete the inline-image;
            6. reinsert the image as a link.

            So far I have this...

            ...

            ANSWER

            Answered 2021-Feb-01 at 10:06

            Thanks to the posts suggested by @Tanaike, the solution I've come up with is as follows. It is very dirty and not well written but it works.

            Workflow...

            1. Get spreadsheet ID and folder ID;
            2. Open a copy of the spreadsheet;
            3. Export as XLSX;
            4. Change filetype to zip;
            5. Unzip into a blob;
            6. Create object to hold xlsx worksheet ids/sheet names, image locations and filenames and Drive image ids for newly created images;
            7. Iterate through each blob in the blob;
            8. Find the xl/workbook.xml file and retrieve sheet id and names;
            9. Find each xl/drawings/drawing#.xml files and retrieve sheet, location and image filename;
            10. Find all images, save to drive and retrieve and map drive ids to filenames;
            11. Go through each sheet in the Google sheet;
            12. Iterate through each cell;
            13. When you find a cell starting with 'com' which ISN'T a formula, generate the image id from the sheet id, row and column, find the corresponding image name and then the corresponding google drive image id.
            14. Clear the cell contents and reinsert as an =IMAGE() formula;
            15. Add a note to the cell with the image name.

            Source https://stackoverflow.com/questions/65966182

            QUESTION

            Oracle - Merge Statement with INSERT and UPDATE
            Asked 2020-Dec-16 at 18:57

            I have an existing table called TextData with fields TextId and Text. In below statement, I am trying to merge(Insert/Update) some records into this table using -

            ...

            ANSWER

            Answered 2020-Dec-16 at 16:50

            I think the (Id, Txt) shouldn't be there as they were.

            Source https://stackoverflow.com/questions/65327451

            QUESTION

            E/Volley: [40176] NetworkDispatcher.processRequest: Unhandled exception java.lang.NullPointerException
            Asked 2020-Dec-16 at 08:09

            I am sending information from my android application to my database by php, however when I execute it and with a spinner I select some of the available options and I give it the following results, I tried to fix it but always says that, I dont know what to do, please help!

            ...

            ANSWER

            Answered 2020-Jul-02 at 06:02

            The problem was that I was passing variables incorrectly with the intent

            Source https://stackoverflow.com/questions/62659153

            QUESTION

            swift build errors from Objective-C app due to import of Objective-C static library that contains a .swift file
            Asked 2020-Dec-07 at 17:22

            I'm importing an ObjC static lib into my ObjC app but get 95 swift-related build errors.
            The ObjC static lib builds ok and contains .m .h and .swift source files.
            Swift file imports CoreBluetooth.

            CONTENTS BELOW...

            1. build errors
            2. source code text
            3. zip of project, in response to kind request from Asperi
              UPDATE 2
              UPDATE 3

            ..1. Here Xcode build errors plus essential source code....................

            ..2. source code text

            ...

            ANSWER

            Answered 2020-Dec-07 at 16:42

            The simplest solution is to allow Xcode to make all dependencies and include all required system libs.

            Here is what I did:

            1. Create workspace at top folder level

            2. Added mobile_sensor_API.xcodeproj to workspace

            3. Added sim_backend_UI.xcodeproj to workspace

            4. Added dependency of sim_backend_UI to lib via workspace

            1. Add Some.swift (any swift file you want) to sim_backend_UI, just for the purpose Xcode add required system swift dynamic libraries (which will be needed for swift part in static library as well)... and confirm creating bridge in appeared dialog

            1. Build >>> Succeeded!

            UPDATE 3 .................................. AFTER I DID THIS ANSWER thru step 6, I got "succeeded" but sim_backend_UI.app is RED and won't run on iphone.

            Source https://stackoverflow.com/questions/65148254

            QUESTION

            Override _prepareSpecificInformation method of \Magento\Payment\Block\Info\Cc class
            Asked 2020-Nov-21 at 13:17

            I want to override _prepareSpecificInformation method of the Magento\Payment\Block\Info\Cc class

            This is Core class.

            vendor/magento/module-payment/Block/Info/Cc.php

            ...

            ANSWER

            Answered 2020-Nov-20 at 10:27

            It turned out that I was overriding a wrong file. Because the \Magento\Payment\Block\Info\Cc was already overridden by a custom module.

            After correcting the preference it worked for me.

            Source https://stackoverflow.com/questions/64782760

            QUESTION

            Android Kotlin Problem parser Gson with Retrofit2 Expected BEGIN_OBJECT but was BEGIN_ARRAY at line 1 column 2 path $
            Asked 2020-Nov-12 at 17:23

            I have a problem when obtaining the json from the Mercadopago demo api and I can't understand what is happening, could you tell me what I am doing wrong?

            and is the "financial_institutions" and "exclusion_pattern" fields modeling well?

            thanks

            JSON

            ...

            ANSWER

            Answered 2020-Nov-12 at 17:22

            Your response should be List , and not MethodsPaymentsResponse containing a list of payments.
            The root of the JSON is an array, not an object that has array variable :)

            Source https://stackoverflow.com/questions/64808238

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

            Vulnerabilities

            No vulnerabilities reported

            Install MAESTRO

            There are two ways to install MAESTRO -- to install the full workflow through Anaconda cloud; or to install only the R codes for exploring the processed data. MAESTRO uses the Miniconda3 package management system to harmonize all of the software packages. Users can install the full solution of MAESTRO using the conda environment. Use the following commands to install Minicoda3:.

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