Comments (4)
from scdrs.
Hi Angelus,
It seems you are using the python scripts which are deprecated. Could you try to rerun the analysis using the scDRS CLI and let us know how it goes? https://martinjzhang.github.io/scDRS/reference_cli.html#compute-score
Thank you,
Martin
from scdrs.
from scdrs.
Hi Angelus,
If you are using log normalized data (size factor + log1p), you need to turn off the raw count flag flag_raw_count False
and the filtering flag --flag_filter False
. Maybe the filtering flag is the reason that scDRS removed many genes/cells.
Also, please double-check that the expression matrix doesn't contain negative values.
Best,
Martin
from scdrs.
Related Issues (20)
- scRNA data input HOT 6
- perform-downstream outputs zero significant cells HOT 1
- plot_group_stats() got an unexpected keyword argument 'plot_kws' HOT 15
- turning off fdr correction HOT 1
- error metaclass conflict HOT 1
- Issues Plotting UMAP from quick start tutorial HOT 1
- gene weights for the control genes HOT 5
- Update dependencies of scDRS
- Gene weights or without gene weights HOT 3
- compute-score is not reading .gs file properly HOT 2
- custom gene set ? HOT 2
- The graphs from a single result and multiple results are inconsistent HOT 13
- Subsetting cells for downstream analysis. HOT 1
- TypeError: '<' not supported between instances of 'str' and 'float' HOT 3
- About compute-score
- Is it reasonable to use human' geneset on mouse scRNAseq data? HOT 2
- TypeError: plot_group_stats() got an unexpected keyword argument 'plot_kws' HOT 16
- trait=z_score: skipped due to small size (n_gene=5, sys_time=116.1s) HOT 1
- AssertionError when running quick test after installation HOT 7
- The 'n_fdr_0.2' number of all group is 0 HOT 7
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 scdrs.