Comments (1)
durenzn
commented on June 24, 2024
For differential expression analysis, people did use count based method like DEseq2 and EdgeR for many years. However, those methods are worse than the simple ranksum test, which take FPKM or CPM as inputs, when the sample size is large. Please see a recent paper from Jingyi Jessica Li’s group: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4
Overall, to perform differential analysis, we just need to use the raw count and normalize it by total read counts, or FPKM/TPM after normalization would work.
from peca.
Related Issues (14)
- matrix dimensions must agree error in matlab HOT 2
- non-model organisms HOT 2
- Request for code clean-up and question about init. of "EM-like" approach HOT 2
- Remove assumption MATLAB is loaded via `Lmod` HOT 3
- Updates on `PECA` and related repositories HOT 2
- lack of CRS part
- Error- Couldn't open motif file
- Does PECA work for uncommon animal species? HOT 1
- Can we use multi-cores to run the programme? HOT 1
- Error when running 'install.sh' HOT 1
- Question: Do you suggest filtering the input gene expression table before running PECA HOT 1
- Undefined function 'fsolve' for input arguments of type 'function_handle' when running `PECA_compare_dif_multiple.sh`
- Question: should I use only nucleosome free region as ATACseq input? 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 peca.