Comments (2)
Hi Wenhao,
I have added the ERCC annotation: https://github.com/LuyiTian/CellBench_data/tree/master/misc.
It should be used with care though. We have noticed the calculated capture efficiency is much lower than we expected and we thought it might be caused by ERCC degradation because there are a couple of freeze-thaw cycles and dilution. Also, we used a very high dilution factor, so as you might see many ERCC genes have a theoretical input lower than one, so cannot be detected even with 100% capture efficiency. personally, I found the methods that use ERCC to separate technical variation do not perform very well, such as BASiCS.
The last thing is that the RNA mixture data were generated from pure RNA instead of cells, where ERCC spike-in behaved well. But the ERCC have more variation in real single-cell data, which might be related to cellular content, as ERCC have short polyA and no secondary structures or attached proteins, making them more vulnerable than cellular mRNA.
from sc_mixology.
Hi @LuyiTian, I see, thank you so much!
Best wishes,
Wenhao
from sc_mixology.
Related Issues (15)
- All the methods tested in the paper all limited in R language? HOT 1
- How to perform log transformation? HOT 3
- some question about clustering HOT 5
- Question regarding 10x UMIs HOT 1
- Is the 10X data 3' or 5'? Which chemistry was used? HOT 1
- can't reproduce the results in the paper HOT 1
- Plans to make into ExperimentHub package? HOT 3
- Number of cells discrepancy HOT 1
- five cancer cell line 10x data barcode+UMI length
- mitochondrial RNA
- known cell grouping variable HOT 2
- Fix encoding(?) of the *_call.R scripts in script/clustering/Clustering_Algorithms HOT 1
- Rdata file contains variables with unclear names HOT 1
- Loading the data from Python HOT 2
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 sc_mixology.