Comments (1)
cbravo93
commented on June 24, 2024
Hi!
Which function are you using exactly? For parameter optimization we use Collapsed Gibbs Sampling, I think this is different in the default sklearn function (they use VEM if I remember correctly?). If you read our paper (https://www.nature.com/articles/s41592-019-0367-1#Sec20), in FigS1 we compared the effect of several parameter estimation methods and found that only collapsed gibbs sampling works well with this type of data.
Cheers!
C
from cistopic.
Related Issues (20)
- Question about createcisTopicObject HOT 1
- installation issue with ubuntu 20.04 HOT 3
- possibility to use BAM files from bulk ChIP HOT 1
- annotateRegions with own dataset HOT 1
- createcisTopicObject and genomic coordinates incompatibility error HOT 3
- input from fragments.tsv.gz? HOT 1
- Installation issue HOT 2
- Tutorial Dataset files HOT 1
- tSNE Clustering Thresholds HOT 1
- How can I run cisTopic in R 4.0 HOT 2
- Ununsed Arguement error in cisTopic/TcisTarget HOT 1
- cisTopicObject <- selectModel(cisTopicObject) Error in .Call("rs_createGD") : C symbol name "rs_createGD" not in load table HOT 1
- Unused argument error while running topicsRcisTarget
- add cisTopic output to Seurat object? HOT 1
- Running Cistopic HOT 1
- Installation error "Failed to install 'unknown package' from Github: ..." HOT 1
- Loading Multiome data
- sha256sum download failed HOT 1
- Error in metadataFeather(path) : Invalid: Not a feather file HOT 3
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 cistopic.