Comments (2)
Potential solution --
Re-implement countReadsPerBin.py
and pass includeLabels=False
to mapReduce
. This should return the chromosome, start and end which will help in sorting the multiprocessing output.
from decoden.
The previous solution does not work. This is the new strategy
- Read in
chrom_sizes.bed
file to get chromosome names and lengths - Call
count_reads_in_region
instead ofrun
. This is still run with multiprocessing, but the results are ordered - Concatenate resulting coverage arrays
from decoden.
Related Issues (20)
- Multiprocessing for preprocessing is not working HOT 1
- Misconfiguration in `run_decoden.py`
- Usage for run_decoden with no arguments HOT 1
- pd.read_csv warnings HOT 1
- Does not work with chromosome names 1, 2, 3, ... HOT 1
- Default argument values contain hardcoded paths
- Missing --conditions argument leads to an obscure error
- Missing HSR_results.ftr file HOT 1
- sklearn warnings HOT 1
- `poetry` needs to be installed before running DecoDen HOT 1
- Installation problems HOT 1
- Data Correlation Heatmap
- `config.json` is empty HOT 1
- Installation fails without some tweaks... HOT 1
- Edits to README HOT 1
- Upgrade from MACS2 to MACS3
- Write processed read in feather format
- Function `get_fragment_length` extracts the tag size instead of the fragment length
- decoden detect fails while parsing experiment_conditions.json
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 decoden.