About
READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010) originating from bacterial samples. Meanwhile is has been extended to process data generated in different experimental setups and from all domains of life. The functions which are accessible via a command-line interface cover read processing and aligning, coverage calculation, gene expression quantification, differential gene expression analysis as well as visualization. In order to set up and perform analyses quickly READemption follows the principal of “convention over configuration”: Once the input files are copied/linked into defined folders no further parameters have to be given. Still, READemption’s behavior can be adapted to specific needs of the user by parameters.
Documentation
Documentation can be found on here.
Installation
Short version (if you have all the requirements installed):
$ pip install READemption
Long version including a description of the requirements and how do you get them.
License
MIT (MIT License) - see LICENSE.txt
Development
If possible follow the principal of “convention over configuration”. This means input file are copied/linked into a fixed location and the resulting files are placed in fixed locations.
The classes should be path agnostic as far a possible. The controller is taking care of that and calls them adequately.
The git braching model is very close to the one proposed here. There two main branches:
master
dev(elopment)
And there are further supporting branches:
feature branches - branched off and back to the dev branch
release branches - branched off from dev and merged back into dev and master
hotfix branches - branched off from master and merged back into dev and master
2 maintainers
Release files for READemption 2.0.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| READemption-2.0.4.tar.gz | 71.4 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| READemption-2.0.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 182.4 kB
Release files / READemption-2.0.4.tar.gz
| Download URL | READemption-2.0.4.tar.gz |
|---|---|
| Size | 71.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.12
|
Release files / READemption-2.0.4-py3-none-any.whl
| Download URL | READemption-2.0.4-py3-none-any.whl |
|---|---|
| Size | 111.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.12
|
