MELD | Quantifying experimental perturbations at single cell | Machine Learning library
kandi X-RAY | MELD Summary
kandi X-RAY | MELD Summary
MELD is a Python package for quantifying the effects of experimental perturbations. For an in depth explanation of the algorithm, please read the associated article:. The goal of MELD is to identify populations of cells that are most affected by an experimental perturbation. Rather than clustering the data first and calculating differential abundance of samples within clusters, MELD provides a density estimate for each scRNA-seq sample for every cell in each dataset. Comparing the ratio between the density of each sample provides a quantitative estimate the effect of a perturbation at the single-cell level. We can then identify the cells most or least affected by the perturbation.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Run clustering
- Compute the smoothed window
- Compute all windows
- Compute the smoothing
- Generate ground truth pdf
- Set the data_phate
- Calculate the EES average
- Fit the graph
- Calculate the EES estimate
- Fits a graph of the graph
- Fit the model to the data
- Calculate the EELD
MELD Key Features
MELD Examples and Code Snippets
Lines of Code : 14License : Non-SPDX (NOASSERTION)
Copy import numpy as np
import meld
# Create toy data
n_samples = 500
n_dimensions = 100
data = np.random.normal(size=(n_samples, n_dimensions))
sample_labels = np.random.choice(['treatment', 'control'], size=n_samples)
# Estimat def find_closest(word, data): # take data as param here
data_with_distance= defaultdict(int)
for key in data:
distance = lev_dist(word, key)
data_with_distance[key] = distance
return {k: v for k, v in sorted(dasection_names = ['Chief Complaint', 'HPI', 'Allergies', 'Last dose of Antibiotics', 'Other ICU medications', 'Other medications', 'Past medical history', 'Family history', 'Social History', 'Occupation', 'Review of systems', 'Physical Examclass Tree():
...
...
def autoscroll(self, sbar, first, last):
...
...
tree = ttk.Treeview(self.frame, columns=("fullpath", "type", "size"),
displaycolumns="size", yscrollcommand=lambda f, l: autosgit config mergetool.meld.path "C:/Program Files (x86)/Meld/Meld.exe"
#!C:/msys64/MINGW32/bin/python3.exe
#!C:/Users/MadPhysicist/AppData/Local/Continuum/anaconda3/python.exe
import fonts_public_pb2
from google.protobuf import text_format
protobuf_file_path = 'METADATA.pb'
protobuf_file = open(protobuf_file_path, 'r')
protobuf = protobuf_file.read()
font_family = fonts_public_pb2.FamilyProto()
text_format.Merif newFileMd5.digest() == existingFileMd5.digest():
...
dir1=
dir2=
outdir=
# copy dir1 to outdir
cp -a $dir1 $outdir
# compare to files in dir2
cd $outdir
find . -type f | while read path; do
# path exists in dir2 and is not different, else delete it
[ -e "$dir2/$path" ] && diff In : df = pd.DataFrame([[1, 2, 3],
[4, 5, 6],
[1, 5, 7]],
columns=['A', 'B', 'C'])
In : df
Out:
A B C
0 1 2 3
1 4 5 6
2 1 5 7
In : Community Discussions
Trending Discussions on MELD
QUESTION
My design has led me into what I think is a complex pytest problem. I'm convinced I don't know the right approach to take. I'm simulating a complex card game, known as 'Liverpool rummy'. The user interface uses Kivy, but the problem I'm having with testing would probably appear with any GUI framework, be it tkinter, QT, wxPython, or whatever.
In rummy simulator, I want to test the logic without actually starting kivy. I think this means that I will need to mock the self in many methods, because the methods call each other via “self.method_name”. My reading of the many posts on mocking self or mocking global or module-level variables has left me pretty confused. I don't want to start kivy for at least two reasons. First, after a whole lot of initialization it'll get to the "play_game" method. While I can call that from code, rather than pushing a button, it'll immediately get a shuffled deck of cards and a discards pile and deal a random hand to the players (all of whom will be robots), who will then each take a turn. But what I need to do for testing is to set those three variables (deck, discard, hand) and run through around 50 variations. Second, that seems to defeat to goal of isolating a unit test as much as possible.
So instead of instantiating the classes, and testing the methods, I'm calling the methods directly from the class. Here is a very simplified example:
...ANSWER
Answered 2022-Mar-22 at 22:32To me, it sounds like you should refactor your code to decouple the game logic from the GUI logic.
I'm of the opinion that the need to use mocks in tests is usually a sign that the code could have been designed better. Here's an article that explains this idea more clearly that I could. One particularly relevant quote:
The need to mock in order to achieve unit isolation for the purpose of unit tests is caused by coupling between units. Tight coupling makes code more rigid and brittle: more likely to break when changes are required. In general, less coupling is desirable for its own sake because it makes code easier to extend and maintain. The fact that it also makes testing easier by eliminating the need for mocks is just icing on the cake.
From this we can deduce that if we’re mocking something, there may be an opportunity to make our code more flexible by reducing the coupling between units. Once that’s done, you won’t need the mocks anymore.
In your case, the tight coupling is between the GUI and the game logic. I'd recommend moving all the game logic into functions/classes that have no connection to the GUI. Ideally, as much logic as possible will end up in pure functions. This will make it much easier to write tests, and to extend/maintain the code down the road.
QUESTION
I am setting up an nginx server with angular universal as front-end and .NET 5 as a back-end API.
ExplanationWhen trying to send a post request to the API i get an net::ERR_CONNECTION_REFUSED error.
You can try it out yourself here: https://modernamedia.no/#kontakt
I have added console.logging for the error.
ErrorError:
...ANSWER
Answered 2022-Mar-06 at 22:10The issue with a lot of API calls is that a browser will tell you it is some kind of CORS error but there is an underlying error that has NOTHING to do with CORS.
However here I think you need to set your client headers to match the backend CORS setup: -
QUESTION
so basically I have a searchbox in my sheet that searches and pulls up data. For a reference see this image: https://i.imgur.com/MVTUCSw.png. So basically in cell A4 I put the data that I am looking for, but my formula restricts me to only looking up stuff in 1 row. For example, data starting with the word MELD, but I would like to be able to also look up data based on for example the someone their name.
The formula I use for the searchbox: =QUERY({'Pallets & Locaties'!A2:G;Voorraadverschillen!A2:G}, "SELECT * WHERE Col1 "&Opzoeken!B4&" '"&A4&"'")
The data that I want to be able to look up is stored in 2 sheets: Pallets & Locaties - https://i.imgur.com/qV7h2tz.png and in Voorraadverschillen - https://i.imgur.com/foqLkKa.png.
The searchbox is only able to lookup data in row, but I just want to be able to search for any kind of stored data in any of the sheets.
Here is my sheet for reference: https://docs.google.com/spreadsheets/d/10wmnxV16JUiD_b_54abkiLPwTqLITWRcUw3gsqvXoBE/edit?usp=sharing
...ANSWER
Answered 2022-Feb-25 at 17:16EDIT:
Cleaned up the formula to not be so repetitive.
=IF(A4<>"",(QUERY({'Pallets & Locaties'!A2:G;Voorraadverschillen!A2:G},"Select * WHERE "&textjoin(" OR ", true, arrayformula("Col"&ROW(1:7)&" "&B4&" '"&A4&"'")))),(QUERY({'Pallets & Locaties'!A2:G;Voorraadverschillen!A2:G},"Select * WHERE Col1 IS NOT NULL")))
This searches every column for the data, as long as data is not identical in two columns you won't have issues. An example would be the search criteria "MELD" being in both Column A and B. If that were the case, only the results from the first matching column would populate.
QUESTION
I am trying to plot a Milestone Trend Analysis with R. At some point, a Milestone is reached and will not be reported anymore. That's also when the line in the graph should stop. So I tried to implement this with ggplot and reshape2 to melt the dataset in a long format:
#edit (Data model by code, sorry) Datamodel:
...ANSWER
Answered 2022-Feb-25 at 14:18To not melt the NA values, set na.rm = TRUE inside the melt() function.
QUESTION
I can compare a current folder state to its latest revision using the following command:
...ANSWER
Answered 2022-Jan-12 at 13:39Preface
Question is offtopic here: as already mentioned in comment, it's question for Software Recommendations site
Face
- Every versioned object with history in SVN can be referenced using PEG-revision for its history state
- Folder in SVN-repo is object of versioning
- In order to compare two folders, you have to have folder-diff tool (for your OS) and know (command-line) options for calling it
According to Slant's comparison:
- Meld can be used on Linux for folder-diffing
- Best folder-diff tool is Beyond Compare
From points 1-3 above it follows that Meld can be used for your task in form
meld folder@REV1 folder@REV2
QUESTION
I have an Expo Managed React Native application. I have some async functions that are called before the main app screen renders. It works perfectly fine on dev mode, production dev mode and Expo Go, but on Test Flight the app immediately hides the Splash Screen.
The long and short of it is that I have a state hook that changes when the AppLoading async method completes. During that async period I update my Context API to include the fetched data from an SQLite database. Here is my code:
...ANSWER
Answered 2022-Feb-07 at 05:48Turns out the issue was that my promise setup was not returning correctly, the proper way to return the promises to not hide the AppLoading component was to change my code to this using Expo Splash Screen and changing my promises like so:
QUESTION
I was trying to use git rebase -i to improv my commits messages. I am the only one working on this director. By mistake, the file opened in the editor became like this:
ANSWER
Answered 2022-Jan-09 at 04:40Assuming you also want to rebase all the way back to the first commit, you should be using:
QUESTION
i'm trying to export a component using export default project; and importing using
import project, {toggleCattegories} from './project';
i get the following warning:
...ANSWER
Answered 2021-Dec-22 at 20:10You are not using Project correctly.
You have a toggleCategories function that should be renamed to render. Class components must have a render function that returns the JSX.
Once you have renamed the above, you no longer import { toggleCategories }, you only need to import Project and where you have , replace it with
QUESTION
I am trying to download some bank statements which only come in .pdf format and convert them to an excel file. I use NitroPDF.exe to convert the .pdf file to an excel file and then have created a VBA script to clean it up and append it into my main Excel file. I have to do the conversion manually up to the point where Excel VBA takes over. I would like to automate it, not sure how. I have tried to use cmd line:
...ANSWER
Answered 2021-Dec-05 at 18:12Always worth quoting file paths, but then you need to escape those quotes in the value being passed to Shell
QUESTION
I use Meld as tool for difftool and mergetool in Git Bash.
When I run git difftool it opens a window of Meld and, every time I close the window with a difference, it opens a new window with the next difference. And so on, they could be hundreds...
Is there a way to stop Meld from the terminal (e.g. I didn't expect all these differences and now I want to make some changes in order to limit the number of them)?
The only way I found is to directly close the terminal, but I'd like a less brutal mode.
ANSWER
Answered 2021-Nov-05 at 15:22Are you tried git config --global --add difftool.prompt false? Or what @Biffen already commented: Ctrl+C in the terminal.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install MELD
You can use MELD like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
