Comments (3)
Hi @Siteng999,
I think you are confusing the terms "lineage" and "condition". There are five experimental conditions, but that does not mean that you should expect 4 lineages (and you almost certainly shouldn't be using the conditions as if they were cell clusters). We use the term "lineage" to mean a single path from a progenitor cell type to a terminal cell type. The number of different terminal cell types is the number of lineages, but it has almost nothing to do with how many experimental conditions are present. I don't know how many lineages would be appropriate for your data, but that has more to do with the biology of the cell system you're studying than with the number of experimental conditions.
Hope this helps clear some things up!
Kelly
from slingshot.
Hello kstreet13
Thank you very much for your reply.
I may need to add some more to the above question. In this experiment I want to obtain the hub-genes of a single tissue cell (e.g. root hair) in response to stimulus specificity. The experimental conditions are sampled in a temporal order under two stimuli. Thus I want to look at single tissues under different time treatments as different states of differentiation. By comparing the differences between the two stimuli at the same sampling time point, I hope to obtain some key signals. Can I solve the above problem when I compare the "lineage" obtained by specifying "start.clus" and "end.clus"?
Sincerely,
siteng
from slingshot.
Sorry!
Now,I have a clear understanding of the above issues. I will close this issue.
Thanks again for your enthusiastic response!
siteng
from slingshot.
Related Issues (20)
- Error in igraph::shortest_paths(tree, from = l, to = ends, mode = "out", : At core/paths/dijkstra.c:360 : Weight vector must not contain NaN values, Invalid value HOT 3
- Average curve weights and Pseudotime HOT 1
- slingshot analysis on PCA but visualization on UMAP HOT 3
- how to analyze with 3 different treatments HOT 4
- how to calclate the POS to compare other algorithm? HOT 2
- Pulling and plotting Differential pseudotime data across different conditions/metadata slots HOT 1
- `embedCurves` should also map MST into new space HOT 1
- Slingshot followed by CellRank HOT 1
- is slingshot using only the variable genes? HOT 2
- Pick one lineage from many for conditiontest HOT 3
- How do I extract feature_info in my rds file? HOT 4
- What does a curve represent biologically? HOT 7
- Overlapping curve issue - change to code needed? HOT 3
- Removing a lineage from a `PseudotimeOrdering` object? HOT 3
- Error in graph.adjacency.dense: Adjacency matrix should be symmetric to produce an undirected graph. Invalid value HOT 5
- pseudotime in two lineage? HOT 2
- Slingshot error HOT 1
- Error while plotting the Minimum Distances Between Cell-Type Centroids using Slingshot in r HOT 6
- Error: (converted from warning) useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE. HOT 1
- Slingshot package ------ Error in crossprod(out) : "crossprod" is not BUILTIN function 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 slingshot.