SCENIC | R package to infer Gene Regulatory Networks | Genomics library

 by   aertslab HTML Version: v1.3.0 License: Non-SPDX

kandi X-RAY | SCENIC Summary

kandi X-RAY | SCENIC Summary

SCENIC is a HTML library typically used in Artificial Intelligence, Genomics, Tensorflow applications. SCENIC has no bugs, it has no vulnerabilities and it has low support. However SCENIC has a Non-SPDX License. You can download it from GitHub.

SCENIC (Single-Cell rEgulatory Network Inference and Clustering) is a computational method to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data. The description of the method and some usage examples are available in Nature Methods (2017). There are currently implementations of SCENIC in R (this repository), and in Python. If you don't have a strong preference for using R, we would recommend to check out the SCENIC protocol repository, which contains the Nextflow workflow, and Python/Jupyter notebooks to easily run SCENIC (highly recommended for running it in batch or bigger datasets). The output from any of the implementations can then be explored either in R, Python or SCope (a web interface).
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            kandi-support Support

              SCENIC has a low active ecosystem.
              It has 283 star(s) with 86 fork(s). There are 22 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 68 open issues and 189 have been closed. On average issues are closed in 281 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of SCENIC is v1.3.0

            kandi-Quality Quality

              SCENIC has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              SCENIC 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.

            kandi-Reuse Reuse

              SCENIC releases are available to install and integrate.
              It has 2810 lines of code, 0 functions and 9 files.
              It has low 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 SCENIC
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            SCENIC Key Features

            No Key Features are available at this moment for SCENIC.

            SCENIC Examples and Code Snippets

            No Code Snippets are available at this moment for SCENIC.

            Community Discussions

            QUESTION

            Android Null Pointer Exception 2 Fragments 1 Activity?
            Asked 2022-Jan-29 at 09:04

            Hi I have a small android app that demonstrates 2 fragments in 1 activity, it should just be a simple code but I am getting a null pointer exception. The app is just a listview in 1 fragment, and an edittext in the other and it connects the main activity. My book is from 2016 so I think some of these things were depreciated that why I am having the error. The text should change in the other fragment after pressing the listview options. Also I am supposed to save the instance state but I haven't got that far yet. I believe the error is from the listener. OnFragmentInteractionListener that it points to null, I can comment the line. Thanks. Code below:

            ...

            ANSWER

            Answered 2022-Jan-29 at 09:04

            if you want to use findById in fragment , you have to add the "view" before them , to add them to view which your returning

            in your onCreateView change :

            Source https://stackoverflow.com/questions/70903532

            QUESTION

            Android App - Error Crashing - ListView SetAdapter
            Asked 2022-Jan-28 at 10:46
                fragment_text.xml
                
                
                
                
                    
                
                
                
                TextFragment.java
                package com.example.tourguide;
                
                import android.content.res.Resources;
                import android.net.Uri;
                import android.os.Bundle;
                
                import androidx.fragment.app.Fragment;
                
                import android.view.LayoutInflater;
                import android.view.View;
                import android.view.ViewGroup;
                import android.widget.ArrayAdapter;
                import android.widget.ListView;
                import android.widget.TextView;
                
                /**
                 * A simple {@link Fragment} subclass.
                 * Use the {@link TextFragment#newInstance} factory method to
                 * create an instance of this fragment.
                 */
                public class TextFragment extends Fragment
                {
                    TextView textView;
                
                
                    // TODO: Rename parameter arguments, choose names that match
                    // the fragment initialization parameters, e.g. ARG_ITEM_NUMBER
                    private static final String ARG_PARAM1 = "param1";
                    private static final String ARG_PARAM2 = "param2";
                
                    // TODO: Rename and change types of parameters
                    private String mParam1;
                    private String mParam2;
                
                    public TextFragment() {
                        // Required empty public constructor
                    }
                
                    /**
                     * Use this factory method to create a new instance of
                     * this fragment using the provided parameters.
                     *
                     * @param param1 Parameter 1.
                     * @param param2 Parameter 2.
                     * @return A new instance of fragment TextFragment.
                     */
                    // TODO: Rename and change types and number of parameters
                    public static TextFragment newInstance(String param1, String param2) 
                    {
                        TextFragment fragment = new TextFragment();
                        Bundle args = new Bundle();
                        args.putString(ARG_PARAM1, param1);
                        args.putString(ARG_PARAM2, param2);
                        fragment.setArguments(args);
                        return fragment;
                    }
                
                    @Override
                    public void onCreate(Bundle savedInstanceState)
                    {
                        super.onCreate(savedInstanceState);
                        if (getArguments() != null)
                        {
                            mParam1 = getArguments().getString(ARG_PARAM1);
                            mParam2 = getArguments().getString(ARG_PARAM2);
                        }
                
                    }
                
                    @Override
                    public View onCreateView(LayoutInflater inflater, ViewGroup 
                    container,
                                             Bundle savedInstanceState)
                    {
                        View view = inflater.inflate(R.layout.fragment_text, container, 
                    false);
                        textView = view.findViewById(R.id.textView1);
                        return view;
                    }
                
                    public void updateTextView(int index)
                    {
                        if(index==0)
                        {
                            
                    textView.setText(getResources().getString(R.string.set_Richmond));
                        }
                        else if(index==1)
                        {
                            
                    textView.setText(getResources().getString(R.string.set_Vancouver));
                        }
                        else if(index==2)
                        {
                            
                    textView.setText(getResources().getString(R.string.set_Toronto));
                        }
                        else if(index==3)
                        {
                            
                    textView.setText(getResources().getString(R.string.set_New_West));
                        }
                        else if(index==4)
                        {
                            
                    textView.setText(getResources().getString(R.string.set_Montreal));
                        }
                        else if(index==5)
                        {
                            
                    textView.setText(getResources().getString(R.string.set_Aldergrove));
                        }
                    }
                
                        public interface OnFragmentInteractionListener
                    {
                        public void onFragmentInteraction(int index);
                    }
                }
                
                fragment_list.xml
                
                
                
                
                    
                
                
                
                package com.example.tourguide;
                
                import android.content.res.Resources;
                import android.net.Uri;
                import android.os.Bundle;
                
                import androidx.fragment.app.Fragment;
                
                import android.view.LayoutInflater;
                import android.view.View;
                import android.view.ViewGroup;
                import android.widget.ArrayAdapter;
                import android.widget.AdapterView;
                
                import android.widget.ListView;
                
                /**
                 * A simple {@link Fragment} subclass.
                 * Use the {@link ListFragment#newInstance} factory method to
                 * create an instance of this fragment.
                 */
                public class ListFragment extends Fragment implements 
                AdapterView.OnItemClickListener
                {
                    ListView listView;
                    String[] array;
                    String listStr;
                    private OnFragmentInteractionListener listener;
                
                
                
                    // TODO: Rename parameter arguments, choose names that match
                    // the fragment initialization parameters, e.g. ARG_ITEM_NUMBER
                    private static final String ARG_PARAM1 = "param1";
                    private static final String ARG_PARAM2 = "param2";
                
                    // TODO: Rename and change types of parameters
                    private String mParam1;
                    private String mParam2;
                
                    public ListFragment() {
                        // Required empty public constructor
                    }
                
                    /**
                     * Use this factory method to create a new instance of
                     * this fragment using the provided parameters.
                     *
                     * @param param1 Parameter 1.
                     * @param param2 Parameter 2.
                     * @return A new instance of fragment ListFragment.
                     */
                    // TODO: Rename and change types and number of parameters
                    public static ListFragment newInstance(String param1, String param2) 
                    {
                        ListFragment fragment = new ListFragment();
                        Bundle args = new Bundle();
                        args.putString(ARG_PARAM1, param1);
                        args.putString(ARG_PARAM2, param2);
                        fragment.setArguments(args);
                        return fragment;
                    }
                
                    @Override
                    public void onCreate(Bundle savedInstanceState) {
                        super.onCreate(savedInstanceState);
                        if (getArguments() != null)
                        {
                            mParam1 = getArguments().getString(ARG_PARAM1);
                            mParam2 = getArguments().getString(ARG_PARAM2);
                        }
                    }
                
                    @Override
                    public View onCreateView(LayoutInflater inflater, ViewGroup 
                    container, Bundle savedInstanceState)
                    {
                        View view = inflater.inflate(R.layout.fragment_list, container, 
                        false);
                        listView = view.findViewById(R.id.listView1);
                        array = 
                        getResources().getStringArray(R.array.string_array_cities);
                        ArrayAdapter adapter = new ArrayAdapter 
                        (getActivity(), android.R.layout.simple_list_item_1, array);
                        listView.setAdapter(adapter);
                        listView.setOnItemClickListener(this);
                        return view;
                    }
                
                    @Override
                    public void onItemClick(AdapterView adapterView, View view, int 
                    index, long id)
                    {
                        if(listener != null)
                        {
                            listener.onFragmentInteraction(index); //pass index of array
                        }
                    }
                
                    public interface OnFragmentInteractionListener
                    {
                        public void onFragmentInteraction(int index);
                    }
                }
                
                activity_main.xml
                
                
                
                
                    
                
                    
                
                
                package com.example.tourguide;
                
                import androidx.appcompat.app.AppCompatActivity;
                import androidx.fragment.app.FragmentManager;
                
                import android.app.Fragment;
                import android.net.Uri;
                import android.os.Bundle;
                
                public class MainActivity extends AppCompatActivity implements 
                TextFragment.OnFragmentInteractionListener, 
                ListFragment.OnFragmentInteractionListener
                {
                
                    @Override
                    protected void onCreate(Bundle savedInstanceState)
                    {
                        super.onCreate(savedInstanceState);
                        setContentView(R.layout.activity_main);
                    }
                
                
                    @Override
                    public void onFragmentInteraction(int index)
                    {
                        FragmentManager manager = getSupportFragmentManager();
                        TextFragment textFragment = 
               (TextFragment)manager.findFragmentById(R.id.fragmentContainerView2_text);
                        textFragment.updateTextView(index);
                    }
                
                }
                
                    strings.xml
                
                    
                    Tour Guide
                    Hello blank fragment
                    default
                    Welcome to the Tour Guide App
                
                    Richmond is a quite city with many nice 
                    hidden scenic places. A small town named Steveston is found on the 
                    south 
                    west part
                    of the city and is well known for having good seafood and nice 
                    places to visit like Garry Point and the west and south dykes. 
                    
                
                    Vancouver is one of Canadas biggest 
                    cities and has a lot to offer like the malls and many towers, 
                    beaches, 
                    parks.
                
                    Toronto is Canadas biggest city on the 
                    east coast and home to the TSX and Maple Leafs.
                
                    New West is a city east of Vancouver but 
                    close by and has nice parks and ice rinks like Moody Park and Queens 
                    Park.
                    Queens Park home of the New West Royals.
                  
                    Monteal is famous for their smoked meat 
                    and they speak french.
                
                    Aldergrove is a quite town and is east 
                    of Langley not too far and is a nice place.
                
                    
                        Richmond
                        Vancouver
                        Toronto
                        New West
                        Montreal
                        Aldergrove
                    
                
                
                
            
            ...

            ANSWER

            Answered 2022-Jan-28 at 10:46

            Everything seems okay only a few lines of code need to be changed.

            Inside TextFragment you need to remove textView initialization from onCreate(...){} method to onCreateView(....) like as follows:

            Source https://stackoverflow.com/questions/70840761

            QUESTION

            How do I change a dataframe in a nested list to a list
            Asked 2021-Nov-03 at 13:15

            I have a data frame with three columns (Category, Sub.category and Acitivty). I need a nested list, with these three levels to put into shinyTree.

            I'm trying to match the format of this .Rds file to create a shinyTree.

            My full table is 99 lines, I've included 30 below, but may need to do over 100+ in the same way.

            So far I've got

            ...

            ANSWER

            Answered 2021-Nov-03 at 13:15

            Here is a possible approach using rrapply() in the rrapply-package to unmelt the data.frame to a nested list:

            Source https://stackoverflow.com/questions/69804732

            QUESTION

            Django TypeError at /brooklyn/beaches
            Asked 2021-Nov-02 at 02:04

            I was given the task to create an NYC Guide project out of Python and Django. I am iterating through a nested dictionary to render boroughs, activities, and venues. The home page lists a handful of boroughs. The boroughs page lists a handful of activities in each borough. The activities page lists a handful of venues to select. My issue is when I click on one of the activities I receive a TracebackError. I am trying to at least render the venues page that has a simple 'VENUES PAGE' on it. I'd love any advice or feedback. This is my first Django project so forgive me if I didn't explain this thoroughly enough. Feel free to ask for further explanation! What I am ultimately trying to do is render an unordered list of venues for each activity in the activities page. I would like each li to be a url that takes me to the venue.html page. It doesn't have to render a specific venue. I can take it from there. I am stuck on this one step. I have already successfully rendered the borough and activities pages, and I have been able to loop through the activities, but when I click on a specific activity I get this error:

            "TypeError at /brooklyn/beaches activity() missing 1 required positional argument: 'venues'"

            ...

            ANSWER

            Answered 2021-Nov-02 at 02:04

            QUESTION

            Comparison of dates in PostgreSQL through Node.js not working
            Asked 2021-Sep-12 at 05:21

            Essentially, I have an a table in a database that is:

            Each row has a stamp_id, timestamp, and title column. All columns are of type 'Text', Collation and Nullable are not defined, storage is 'extended' for all. In this particular row,

            ...

            ANSWER

            Answered 2021-Sep-12 at 05:21

            Your schema defines the timestamp column as type text. The timestamp text you pass in from nodejs use a different format, in particular, your example shows that hours is not zero padded. This means your timestamps string (hours) do not compare the way you expect:

            Source https://stackoverflow.com/questions/69148487

            QUESTION

            I can't Upload Images from React to Django backend
            Asked 2021-Aug-18 at 11:03

            I am trying to give a user the possibility to add an Image to their post when they sent a post request in the CreatePost component in my react frontend.

            This is the object I sent to the backend from React ]}>

            Here is the full error I'm getting when trying to serialize it in the view.

            ...

            ANSWER

            Answered 2021-Aug-18 at 00:39
            return Response(Serializer.errors,status=status.HTTP_400_BAD_REQUEST)
            

            Source https://stackoverflow.com/questions/68809244

            QUESTION

            How to calculate ratio of values in a pandas dataframe column?
            Asked 2021-Aug-16 at 02:51

            I'm new to pandas and decided to learn it by playing around with some data I pulled from my favorite game's API. I have a dataframe with two columns "playerId" and "winner" like so:

            ...

            ANSWER

            Answered 2021-Aug-16 at 02:13

            You can try something like this

            Source https://stackoverflow.com/questions/68796549

            QUESTION

            Recyclerview view not displaying list item correctly
            Asked 2021-Jun-24 at 19:34

            Screenshot of the recyclerview I want the image view width to be match parent, but I am not able to understand what is wrong? I have set that base element to match parent and then add constraint to be match parent, but on running the code the list items are not constrained to the parent.Any help would be helpful.

            RecyclerView:

            ...

            ANSWER

            Answered 2021-Jun-24 at 19:34

            When you are inflating a view in onCreateViewHolder, you have to specify ViewGroup as parent.

            Try changing

            FavouritesViewHolder(MemesListItemBinding.inflate(LayoutInflater.from(parent.context)))

            To

            FavouritesViewHolder(MemesListItemBinding.inflate(LayoutInflater.from(parent.context), parent, false))

            Source https://stackoverflow.com/questions/68121432

            QUESTION

            Databinding: "unresolved reference" for variable name
            Asked 2021-Apr-10 at 20:11

            I cannot usage databinding for activity. (I used databinding for fragment/recyclerview).

            I researched all documents and all issues but it didn't solve my problem.

            My problem is "unresolved reference" for variable name in xml file. Where is the problem in my project.

            DetailActivity.kt

            ...

            ANSWER

            Answered 2021-Apr-10 at 20:04

            The problem is that you reference a binding class of the MainActivity which is (ActivityMainBinding) to the DetailActivity.

            Therefore, it can't find a setResult() method in the ActivityMainBinding, because there is no result variable in activity_main.xml layout.

            Notice that each activity has a unique generated class that bounds to its own layout.

            To fix this you need to replace ActivityMainBinding with ActivityDetailBinding

            Source https://stackoverflow.com/questions/67038630

            QUESTION

            How to replace or remove special characters from scrapy?
            Asked 2021-Apr-01 at 12:07

            I just started learning scrapy and trying to make spider to grab some info from website and trying to replace or remove special characters in 'short_descr'

            ...

            ANSWER

            Answered 2021-Apr-01 at 12:07

            If you're removing these special characters just because they appear weirdly in a CSV file, then I suggest not removing them. Just simply add the following line in the settings.py file.

            Source https://stackoverflow.com/questions/66897785

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

            Vulnerabilities

            No vulnerabilities reported

            Install SCENIC

            You can download it from GitHub.

            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 .
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            gh repo clone aertslab/SCENIC

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