Comments (1)
Hi,
My understanding is that fine.tuning in SingleR just classifies cells into more nuanced cellular phenotypes, but does not change the results of the main cell type classifications. Nonetheless, when I set fine.tune = TRUE, I saw a pretty common mistake in automatic classifiers: many flow sorted T cells (CD3+) were annotated by SingleR as NK cells. It can be difficult to discern collinear T cell subsets; often classifiers mistake T cells for NK cells. SignacX had strong performance in this space; but the flow sorted data in that cohort was just for four populations: T, B, monocytes and fibroblasts, so that is the ground truth that I used.
Hope this helps!
Best regards,
Mathew
from signacx.
Related Issues (20)
- Warning messages in Signac() and then Error in GenerateLabels() HOT 8
- down load problem with Signac HOT 6
- Error in CID.LoadEdges(data.dir = spring.dir) HOT 5
- New issues running Signac X on Seurat objects HOT 6
- Using small number of markers (n= 47) returns error HOT 1
- The code is trying to access objects that does not exist in the dataset HOT 1
- rbind error in SignacBoot function HOT 2
- How to reproduce HPCA training data
- Seurat v4.3.0 compatibility issue HOT 1
- Benchmarking SignacX vs SingleR in PBMC?
- Error in res[[j - 1]] : attempt to select less than one element in get1index <real> HOT 1
- How to apply SignacX to mouse dataset?
- Can SignacX also automatically annotate platelets too?
- Signac or SignacFast hang HOT 1
- Prepare for upcoming Seurat v5 release
- Downloading raw data used for SignacX
- Cholmod error 'problem too large' HOT 3
- Run Error HOT 4
- Issues running Signac on newer Seurat objects HOT 4
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 signacx.