Comments (5)
This looks like exactly what we need 😍 :
https://github.com/becavin-lab/checkatlas
Example QC report:
https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_2/CheckAtlas_example_2.html
from scrnaseq.
The cellranger multiqc module has been merged, example:
https://github.com/ewels/MultiQC/files/10086650/multiqc_report_cellranger.html.zip
The checkatlas example multiqc reports start looking more mature now as well:
https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_2/CheckAtlas_example_2.html
We should probably add both!
from scrnaseq.
Looks really beautiful - also nice that we could integrate it into MultiQC directly so it is all in one nice report 👍🏻
from scrnaseq.
MultiQC PR is still open 👍🏻 MultiQC/MultiQC#1713
from scrnaseq.
There's also a multiqc module for cellranger:
MultiQC/MultiQC#1689
from scrnaseq.
Related Issues (20)
- Sample merging does not work if files are named the same
- 'star' in genome configrations ignored HOT 2
- Cellranger mkref resource flags incorrect HOT 3
- Error with CONCAT_H5AD HOT 3
- Running 'cellranger-arc count' with existing genome index
- cellranger-multi implementation follow-up
- Trimming R1 fast files in all aligners HOT 4
- Time limit of AlevinQC HOT 3
- Specify cellranger version HOT 1
- scrnaseq will not recognize my genome file path HOT 2
- `--cellranger_index` only appears to work if `--validate_params false` provided HOT 3
- cellranger_count.py: capture stderr and stdout HOT 4
- Implement sample demultiplexing followed by VDJ + feature barcode analysis per sample HOT 5
- pipeline not compatible with nextflow 23 => PosixFileAttributeView HOT 1
- cellranger count => Your reference does not contain the expected files HOT 2
- Error while excuting emptydrops HOT 1
- nextflow inspect does not work due to missing parameters HOT 2
- Support for 10x Gem-X V4 libraries HOT 5
- Tests are not executed HOT 3
- Standardize h5ad/seurat var gene annotations across aligners HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from scrnaseq.