SCENIC | R package to infer Gene Regulatory Networks | Genomics library
kandi X-RAY | SCENIC Summary
kandi X-RAY | SCENIC Summary
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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QUESTION
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 09:04if 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 :
QUESTION
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 10:46Everything 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:
QUESTION
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 13:15Here is a possible approach using rrapply()
in the rrapply
-package to unmelt
the data.frame to a nested list:
QUESTION
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 02:04URLS.PY
QUESTION
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 05:21Your 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:
QUESTION
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 00:39return Response(Serializer.errors,status=status.HTTP_400_BAD_REQUEST)
QUESTION
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 02:13You can try something like this
QUESTION
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 19:34When 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))
QUESTION
ANSWER
Answered 2021-Apr-10 at 20:04The 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
QUESTION
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 12:07If 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.
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