CITE-seq-Count | get UMI counts from a single cell protein | Genomics library

by Hoohm Python Version: 1.4.5 License: MIT

X-Ray Key Features Code Snippets(1)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | CITE-seq-Count Summary

CITE-seq-Count is a Python library typically used in Artificial Intelligence, Genomics applications. CITE-seq-Count 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 CITE-seq-Count' or download it from GitHub, PyPI.

A tool that allows to get UMI counts from a single cell protein assay

Support

Quality

Security

License

Reuse

Support

CITE-seq-Count has a low active ecosystem.

It has 50 star(s) with 30 fork(s). There are 12 watchers for this library.

It had no major release in the last 12 months.

There are 24 open issues and 122 have been closed. On average issues are closed in 87 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of CITE-seq-Count is 1.4.5

Quality

CITE-seq-Count has 0 bugs and 0 code smells.

Security

CITE-seq-Count has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

CITE-seq-Count code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

CITE-seq-Count 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

CITE-seq-Count releases are available to install and integrate.

Deployable package is available in PyPI.

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

Installation instructions, examples and code snippets are available.

CITE-seq-Count saves you 457 person hours of effort in developing the same functionality from scratch.

It has 1079 lines of code, 50 functions and 10 files.

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

Top functions reviewed by kandi - BETA

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

Parse command line arguments
Maps two reads
Given a sequence of tags find the matching tag
Find the most mapped tag from tags
Create a report summary report
Convert seconds to text
Return plural plural form
Performs a single cell correction
Collapse cell barcodes
Given a whitelist of blacklisted cells and a whitelist and a whitelist for each cell
Finds a mapping of barcodes to true to false
Performs the UMIS on the final results
Calculate the counts for all UMI clusters
Generate a list of n_reads
Calculate start and stop indices based on chunk size
Count the number of lines in a file
Generate blocks of given size

Get all kandi verified functions for this library.

CITE-seq-Count Key Features

No Key Features are available at this moment for CITE-seq-Count.

CITE-seq-Count Examples and Code Snippets

CITE-seq-Count,Installation

Python

Lines of Code : 1

License : Permissive (MIT)

Copy

pip install CITE-seq-Count==1.4.4

Community Discussions

Trending Discussions on CITE-seq-Count

Pip install fails at building wheel at subpackage?

QUESTION

Pip install fails at building wheel at subpackage?

Asked 2019-Nov-13 at 11:55

Somewhat a beginner at coding. I was looking to install a package using pip install that I was able to get before I updated my python (currently have Python 2.7.16 and 2.8.0 on my Mac).

The package I am trying to install is called CITE-seq-Count (https://hoohm.github.io/CITE-seq-Count/Installation/)

I have tried their recommended installation:

...

ANSWER

Answered 2019-Nov-13 at 11:55

It's an issue in pysam which seems to be not yet fully compatible with Python 3.8. There is already a github issue for this problem, might be worth following it to see if a solution turns up: https://github.com/pysam-developers/pysam/issues/860

For now, falling back to Python 3.7 could be the easiest solution if you don't depend on 3.8 features (worked for me).

Source https://stackoverflow.com/questions/58828857

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

Vulnerabilities

No vulnerabilities reported

Install CITE-seq-Count

The official documentation can be found here.

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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