prstools
prstools is software to create Polygenic Risk Scores (PRS) directly
from the commandline.
It makes PRS generation easier, compared to previous tools, by:
- Super fast reading and matching of sumstats (handles odd formats).
- Rapid creation of the model.
- Automatic generation of the PRS Prediction for target plink files.
All the above, for a real GWAS sumstat, within 30 minutes using only 1 command. Installation and running the demo example should not take more than 10 minutes.
Website: https://prstools.readthedocs.io/
Install
To install use the following command.
pip install -U --prefer-binary prstools
For it to work, you should have python3.8 or later installed (pip is
included in python3.8+). If the command above does not work directly you
can install using conda (or mamba if you have that) by running
conda install "python>=3.9". For other install issues please check the
install
guide
or send us a mail.
How to use
Immediately after installing prstools, it should be possible to download & run the demo example (~4mb), by pasting the following into the commandline:
# Makes 'example' dir with data in current path:
prstools downloadutil --pattern example --destdir ./; cd example
# Run the model with example data:
prstools prscs2 --ref ldref_1kg_pop --target target \
--sst sumstats.tsv --n_gwas 2565 --out ./result
This will run PRS-CS2 and make PRS prediction using example data. For a
more comprehensive introduction and the best and fastest way to get a
PRS for your case, try the Getting Started
Tutorial.
Additionaly, prstools provides documentation through its command-line
interface. Run prst to see the available commands, or
prst prscs2 --help for options and copy-pastable examples. The same
documention is available
online too.
Tutorial + Video
For more information and a hands-on demonstration of what prstools can
do, have a look at the Getting Started
Tutorial.
There is also a Video. The
tutorial+video is a tiny bit older than the current prstools version,
which has more functionality. You can load the tutorial in a free cloud
instance by clicking here: 
Contact
For questions and support please send a mail (menno.j.witteveen@gmail.com).
We are actively developing prstools and feedback by mail or our feedback form (with 🏆 lottery) is much appreciated!
1 maintainer
Metadata
1 maintainer
Release files for prstools 0.0.83
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| prstools-0.0.83.tar.gz | 2.0 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| prstools-0.0.83-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 4.0 MB
Release files / prstools-0.0.83.tar.gz
| Download URL | prstools-0.0.83.tar.gz |
|---|---|
| Size | 2.0 MB |
| Tags | Source |
|
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.11.4
|
Release files / prstools-0.0.83-py3-none-any.whl
| Download URL | prstools-0.0.83-py3-none-any.whl |
|---|---|
| Size | 2.0 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.11.4
|
