scAI | unsupervised approach for the integrative analysis | Genomics library

 by   sqjin R Version: v1.0.0 License: GPL-3.0

kandi X-RAY | scAI Summary

kandi X-RAY | scAI Summary

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

Once the single cell multi-omics data are decomposed into multiple biologically relevant factors, the package provides functionality for further data exploration, analysis, and visualization. Users can:. Check out our paper (Suoqin Jin#, Lihua Zhang# & Qing Nie*, Genome Biology, 2020) for the detailed methods and applications.
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              scAI has a low active ecosystem.
              It has 13 star(s) with 4 fork(s). There are 1 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 3 open issues and 6 have been closed. On average issues are closed in 25 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of scAI is v1.0.0

            kandi-Quality Quality

              scAI has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              scAI 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

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

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            scAI Key Features

            No Key Features are available at this moment for scAI.

            scAI Examples and Code Snippets

            copy iconCopy
            if(!require(devtools)){ install.packages("devtools")}
            install.packages("RcppEigen")
            devtools::install_github("jaredhuling/rfunctions")
            
            library(devtools)
            install_github('linxihui/NNLM')
            install_github("yanwu2014/swne")
            install_github("jokergoo/Comple  
            copy iconCopy
            object <- selectFeatures(object, assay = "RNA")
            object <- run_scAI(object, K, do.fast = TRUE, hvg.use1 = TRUE)
            
            object <- selectFeatures(object, assay = "RNA")
            loci.use <- searchGeneRegions(genes = object@var.features[[1]], species = "mou  
            copy iconCopy
            sudo installer -pkg \
            /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \
            -target /
              

            Community Discussions

            QUESTION

            How to get a {{geocodeArea: xxx }} query to work in python using overpy?
            Asked 2019-Oct-02 at 00:23

            I want to find all pubs in a specific area using the Overpass API and selecting the area with geocodeArea.

            Testing the following query on overpass-turbo.eu gives me the desired result:

            ...

            ANSWER

            Answered 2018-Sep-10 at 09:15

            {{geocodeArea: xxx }} is a special feature of overpass turbo and not part of Overpass API. overpy uses Overpass API directly which means you can't use this keyword.

            However {{geocodeArea: xxx }} just tells overpass turbo to perform a geocoding request, i.e. transform an address into a geographic location. You can do the same, e.g. by making a call to Nominatim, Photon or any other geocoder.

            Source https://stackoverflow.com/questions/52236655

            QUESTION

            How to use optimizer.minimize with maxPooling layers in TensorFlow.js
            Asked 2019-Feb-03 at 22:54

            When using optimizer.minimize() with model.predict() to train a model with a loss function in TensorFlow.js, I encounter an issue. This only occurs when I use a maxPooling2D layer in a convolutional neural network with code similar to the code below. It produces this error: Cannot read property 'backend' of undefined. I'm not sure what is causing this or how to resolve it. The error does not occur when using a convolutional layer (tf.layers.conv2d()) without any pooling layers. I'm using TensorFlow.js version 0.14.2 and Google Chrome version 71.0.3578.98. This error can be reproduced using the following code:

            ...

            ANSWER

            Answered 2019-Feb-02 at 19:10

            In TensorFlow.js 0.14+, there is a change that disables backpropagation support in the Model.predict() method. You can use the Model.apply() method with the {training: true} flag to fix your code.

            I.e., change

            Source https://stackoverflow.com/questions/54493359

            QUESTION

            Plotting unsorted way/area's node reference from .osm file
            Asked 2018-Oct-29 at 09:18

            So i am trying to define an exact shape (outter layer) of a building from .osm node references because I need to create more detail structure inside it (rooms, walls) based of some assumption.

            Until now I've extracted the node's coordinate from its reference of 'building:part' using pyosmium, stored the node's coordinates to a list of tuples, reconstructed it using Polygon function from shapely and plotted it using mplleaflet. But somehow the nodes from the reference aren't sorted and when I try to plot it, there are a lot of intersections shown.

            My current method to solve this sorting problem is following:

            ...

            ANSWER

            Answered 2018-Jun-14 at 09:12

            Nodes are referenced by ways in the correct order, i.e. so that they are adjacent to each other. You don't need to perform any manual sorting if you read the list of referenced node IDs correctly. Manual sorting is only required for relation elements.

            Unfortunately I'm not familiar with pyosmium so I can't tell you what's wrong with your code.

            Source https://stackoverflow.com/questions/50852455

            QUESTION

            How to return Document Index Name Value
            Asked 2018-Oct-03 at 13:35

            This is a GoLang, Firebase AdminSDK question.

            This example works to iterate through all of the documents in a FireStore DB.

            How can I get the Document Name?

            To put another way: If the collection name is JohnyCollection, and JohnyCollection has 20 Documents called (Document1, Document2.... Document20), how do I get the document name in golang Code?

            //========================================

            ...

            ANSWER

            Answered 2018-Oct-03 at 13:35

            You can get the document ID from the DocumentSnapshot, by first looking up the DocumentRef:

            Source https://stackoverflow.com/questions/52626974

            QUESTION

            Order By Lowest Value in total column, by year with GROUP BY on another column
            Asked 2017-Jun-28 at 23:11

            My Table looks like the following:

            Am using the following query to output this data in a table (front-end):

            ...

            ANSWER

            Answered 2017-Jun-28 at 18:46

            QUESTION

            running mail doc, server link not working properly
            Asked 2017-Jun-16 at 13:05

            Problem :

            1. Using Agent run and send mail give a different link

            2. Mail Contain a link which is not include database

            3. I set it send to a yahoo mail

              ...

            ANSWER

            Answered 2017-Jun-16 at 11:34

            First of all: Sending an external mail with a custom form like you do it is not the best Idea, as the target system might not be able to render everything accordingly.

            That said, I would first create a document that contains all data and then RENDER it to a maildoc. code would look like this:

            Source https://stackoverflow.com/questions/44586842

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

            Vulnerabilities

            No vulnerabilities reported

            Install scAI

            Download source codes here and type (in R). This website shows other ways for building and installing an R package.
            Troubleshooting: Installing RcppEigen and rfunctions on R>=3.5 requires Clang >= 6 and gfortran-6.1. For MacOS, it's recommended to follow guidance on the official R page here OR the post. For Windows, please ensure that Rtools is installed. scAI provides functionality for further data exploration, analysis, and visualization. A couple of excellent packages need to be installed. Using UMAP and FIt-SNE is recommended for computational efficiency when using reducedDims on very large datasets. -- install UMAP Python package: pip install umap-learn. Please check here if there is any trouble. -- install FIt-SNE R package: Installing and compiling the necessary software requires the use of FIt-SNE and FFTW. For detailed instructions of installation, please visit this page.
            Please consider install RcppEigen and rfunctions if they are not automatically installed.
            Install other dependencies
            Install Leiden algorithm for identifying cell clusters: pip install leidenalg. Please check here if there is any trouble.
            Install UMAP and FIt-SNE for faster dimension reduction in reducedDims

            Support

            If you get the error "clang: error: unsupported option '-fopenmp'" when installing R package, please consider the configuration in ~/.R/Makevars and see this post for detailed configuration. In addition, you may can also reinstall your R because -fopenmp option is usually added by R automatically if openmp is available.
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