starfish | starfish : unified pipelines for image-based transcriptomics | Genomics library

by spacetx Python Version: 0.2.2 License: MIT

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | starfish Summary

starfish is a Python library typically used in Artificial Intelligence, Genomics applications. starfish has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install starfish' or download it from GitHub, PyPI.

starfish: unified pipelines for image-based transcriptomics

Support

Quality

Security

License

Reuse

Support

starfish has a low active ecosystem.

It has 172 star(s) with 55 fork(s). There are 17 watchers for this library.

It had no major release in the last 12 months.

There are 150 open issues and 525 have been closed. On average issues are closed in 97 days. There are 13 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of starfish is 0.2.2

Quality

starfish has 0 bugs and 0 code smells.

Security

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

starfish code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

starfish is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

starfish releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

starfish saves you 10114 person hours of effort in developing the same functionality from scratch.

It has 20585 lines of code, 1195 functions and 357 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed starfish and discovered the below as its top functions. This is intended to give you an instant insight into starfish implemented functionality, and help decide if they suit your requirements.

Display an image stack
Mask the low intensity values in the given intensity threshold
Expand a max intensity table
Normalize axes
Return a setuptools cmdclass
Create a ConfigParser from a root
Get the project root directory
Extract version information from setup py
Process fov field
Get a slice from a selector
Prepares a sequence of stages
Overrides an image stack
Get a slice of the given selector
Get spot attributes from target image
Given a tileset return a list of CropParameters
Measure the locations of spot locations in the image
Runs the model
Extract version information from VCS
Sets up the main map
Runs the processing pipeline
Download example data files
Set a slice
Write an experiment JSON file
Apply a function to the stack
Create the versioneer config file
Format a structured dataset
Convert an image to a list of spot objects

Get all kandi verified functions for this library.

starfish Key Features

No Key Features are available at this moment for starfish.

starfish Examples and Code Snippets

No Code Snippets are available at this moment for starfish.

Community Discussions

Trending Discussions on starfish

Marker Interface vs Enums

How do I join with multiple SQL tables and return one row per base table record with the correct GROUP_CONCAT data?

Discord.js Embed reactions for another embed

displaying Mandelbrot set in python using matplotlib.pyplot and numpy

Actionscript: How can I create a counter that registers a hitTestObject and shows the score on the main stage?

Python Slot Machine: Calculating Line Payouts

How To get specific data from mysql in NodeJs REST API

Java - Polymorphism : legal vs illegal declarations

Why can't I colour my segmented region from the original image

Java.lang.Object; cannot be cast to

QUESTION

Marker Interface vs Enums

Asked 2021-Apr-17 at 11:36

I am trying model a zoo.

Suppose I have the following structure for areas in the Zoo(omitted some details)

...

ANSWER

Answered 2021-Apr-17 at 10:53

I would use enums. You don't need all of those if statements.

Just have the attribute type in both Animal and AnimalHabitat and then compare them.

Source https://stackoverflow.com/questions/67136837

QUESTION

How do I join with multiple SQL tables and return one row per base table record with the correct GROUP_CONCAT data?

Asked 2020-Dec-11 at 17:13

I have a situation where I want to join multiple SQL tables and get back one row per record in the base table as well as GROUP_CONCAT the other table data together with |. Unfortunately, with the query method I'm currently using, I'm getting back undesired multiplicity in the GROUP_CONCAT data and I don't know how to solve it.

I have the following basic DB structure:

...

ANSWER

Answered 2020-Dec-11 at 17:13

You are concatenating along two separate dimensions. The simplest solution is DISTINCT:

Source https://stackoverflow.com/questions/65255509

QUESTION

Discord.js Embed reactions for another embed

Asked 2020-Apr-22 at 06:26

I'm trying to catch reactions to make the bot send another embed

...

ANSWER

Answered 2020-Apr-22 at 01:35

You are going to have to use .createReactionCollector() to collect the reaction and send the embed when the reaction collector collects a specific emoji.

You can read this guide to understand reaction collectors more.

Source https://stackoverflow.com/questions/61355836

QUESTION

displaying Mandelbrot set in python using matplotlib.pyplot and numpy

Asked 2020-Mar-01 at 02:27

I am trying to get a plot of a Mandelbrot set and having trouble plotting the expected plot.

As I understand, the Mandelbrot set is made up of values c, which would converge if are iterated through the following equation z = z**2 + c. I used the initial value of z = 0.

Initially, I was getting a straight line. I look for solutions online to see where I went wrong. Using the following link in particular, I attempted to improve my code:

https://scipy-lectures.org/intro/numpy/auto_examples/plot_mandelbrot.html

Here is my improved code. I don't really understand the reason of using np.newaxis and why I am plotting the final z values that converge. Am I misunderstanding the definition of the Mandelbrot set?

...

ANSWER

Answered 2020-Feb-29 at 21:58

The plot doesn't look correct, because in the code in the question z (i.e. the iterated variable) is plotted. Iterating z = z*z + c, the Mandelbrot set is given by those real, imaginary part pairs of c, for which the series doesn't diverge. Hence the small change to the code as shown below gives the correct Mandelbrot plot:

Source https://stackoverflow.com/questions/60467316

QUESTION

Actionscript: How can I create a counter that registers a hitTestObject and shows the score on the main stage?

Asked 2019-Apr-28 at 15:24

My game counts the number of hits to an object and brings the user either to a winning or losing page. How can my hitTestObject count the number of hits while showing the number on the main stage? If the user hits "friend" 5 times, I want it to play the "youWin" layer and if they hit a "biter" once, I want it to play the "youLose" layer. (Please help this is for my final project and I'm almost done) Thank you! :)

...

ANSWER

Answered 2019-Apr-28 at 15:24

You need many updates in your code, but I'll try to copy and paste your code with small modifications. You should define your variables outside of for loop, also you must add multiple objects like 'friends' to an array.

Source https://stackoverflow.com/questions/55883432

QUESTION

Python Slot Machine: Calculating Line Payouts

Asked 2019-Mar-13 at 15:37

I'm a Python newbie attempting to create a slot machine simulator that mimics the payouts of the real machines. I'm running into an issue in calculating the line payouts, and I'm sure there's a smarter way of iterating through the lines and calculating them.

Defining some constants that I'll be using:

...

ANSWER

Answered 2019-Mar-13 at 15:37

You need to use the global keyword in each function to access variables defined in a parent. For example:

Source https://stackoverflow.com/questions/55145090

QUESTION

How To get specific data from mysql in NodeJs REST API

Asked 2018-Sep-07 at 10:25

Here is my database:

Here is my code

...

ANSWER

Answered 2018-Sep-07 at 10:25

TRY THIS

Source https://stackoverflow.com/questions/52219794

QUESTION

Java - Polymorphism : legal vs illegal declarations

Asked 2018-May-07 at 18:25

                                      ANIMAL
                                  /           \
                      VERTEBRATE             INVERTEBRATE
                     /     |     \           /     |     \
                   CAT    DOG    COW      SPIDER  ANT   CORAL
                  /   \
          COLOR_SOLID CALICO

...

ANSWER

Answered 2018-May-07 at 18:25

You are correct.

Source https://stackoverflow.com/questions/43838553

QUESTION

Why can't I colour my segmented region from the original image

Asked 2018-Feb-28 at 07:15

I have the following code:

...

ANSWER

Answered 2018-Feb-27 at 22:03

Your code is kinda confusing... I don't understand whether the mask you want to use is starS or result since both look like 2d indexers. In your second code snippet you used starS, but the mask you posted in your question is result.

Anyway, no matter what your desired mask is, all you have to do is to use the imoverlay function. Here is a small example based on your code:

Source https://stackoverflow.com/questions/49018022

QUESTION

Java.lang.Object; cannot be cast to

Asked 2017-Oct-18 at 14:43

So - I'm new to hiberate and Java in general. I've seen a couple threads in regards to this error, but none seem to fit my situation. I have a simple JPQL query as shown below that should returnthe function ID and name from the Function table/entity. This query is held within my FunctionRepository.java

...

ANSWER

Answered 2017-Oct-18 at 14:35

You are only selecting two fields of your entities:

Source https://stackoverflow.com/questions/46812684

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

Vulnerabilities

No vulnerabilities reported

Install starfish

You can install using 'pip install starfish' or download it from GitHub, PyPI.
You can use starfish 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

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 .

Find more information at: