semvec/pypi-packages huggingface dataset:
iCount-Mini 3.0.1
Computational pipeline for analysis of iCLIP data
License: MIT
Keywords: iCLIP protein-RNA

# iCount-Mini

This is a fork of iCount maintained by members of [Jernej Ule's](http://ulelab.info) group, focussing on the peak calling features of iCount.

Run commands using:
`iCount-Mini <command>`

**Note on small differences of terminology between iCount-Mini and iCount**
+ In iCount-Mini, sigxls = iCount peaks and iCount-Mini peaks = iCount clusters. This is to bring the terminology more in line with the rest of the field.
+ In iCount-Mini RNA-maps have been renamed to 'metagene', to distinguish these plots which include only CLIP data from other RNA-maps which group crosslinks into categories dependent on orthogonal data, such as alternatively spliced exons.

# iCount: protein-RNA interaction analysis

iCount is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions and generate:
 
+ demultiplexed and adapter-trimmed FASTQ files
+ BAM files with mapped iCLIP reads
+ identified protein-RNA cross-linked sites, saved to BED files
+ statistically significant cross-linked sites, saved to BED files
+ peaks of significant cross-linked sites, saved to BED files
+ grouping of individual replicate experiments
+ metagene generation showing the positional distribution of cross-linked sites relative to genomic landmarks
+ kmer enrichment analysis

You may start with the [tutorial](http://icount.readthedocs.io/en/latest/tutorial.html) or dive into the 
[documentation](http://icount.readthedocs.io/en/latest/index.html).

## iCount-Mini Authors

iCount-Mini is maintained by members of [Jernej Ule's](http://ulelab.info) group.

## iCount Authors

iCount is developed and supported by [Tomaž Curk](http://curk.info) from the [Bioinformatics Laboratory](http://biolab.si) at the [University of Ljubljana](http://www.uni-lj.si), [Faculty of Computer and Information Science](http://www.fri.uni-lj.si) and in collaboration with the laboratory of [Jernej Ule](http://ulelab.info).

The development started in late 2008 when Tomaž Curk and Gregor Rot wrote a first prototype of iCount.
In mid-2016, [Jure Zmrzlikar](https://github.com/JureZmrzlikar) from [Genialis](http://www.genialis.com) helped refactoring and improving the code, which is now available here.

## Development

To install a development version of iCount-Mini, use this command.
It's recommended to do this within a Python virtual environment.

```bash
pip install --upgrade -r requirements-rtd.txt -e .
```
pplmyapi 0.0.7
Python client for PPL myAPI
License: MIT
Requires Python: >=3.6

# 📦📦 pplmyapi (Python PPL myAPI wrapper) 
Czech PPL (Professional Parcel Logistic) API wrapper written in Python. Helps you to communicate with PPL myAPI without worring about fetching access tokens and constructing your own requests. All (hopefully) done for you in the background.

# Install it from PyPI
```bash
pip install pplmyapi
```

## Usage
This is still a work in progress, so the API might change in the future. However, the basic usage is as follows:
1. Create a `PPL` instance with your credentials
2. obtain a `RESTConnector` instance from the `PPL` instance.
3. use the `RESTConnector` instance to communicate with the PPL REST API (myAPI2)

### Send a package
```python
# Create Package instance with all the required data and 6 packages in the set
package = Package(
    reference_id="123456789",
    package_product_type=Product.PPL_PARCEL_CZ_PRIVATE_COD,
    note = "test",
    recipient=Recipient(
        name="John Doe",
        city="Hradec Králové",
        street="Hlavní 1",
        zip_code="50001",
        phone="123456789",
        email="j.doe@example.com",
        country = 'CZ'
    ),
    sender=Sender(
        name="Test s.r.o.",
        street="Testovací 55/36",
        city="Praha",
        zip_code="11000",
        country="CZ",
    ),
    payment_info=PaymentInfo(
        cod_price=100,
        cod_currency='CZK',
        cod_vs='123456789',
        insurance_price=100,
        insurance_currency='CZK',
        specific_symbol='123456',
        bank_account='123456789',
        bank_code='0300'
    ),
    weighted_package_info=WeightedPackageInfo(
        weight=10.22,
    ),
    package_set=(
        PackageSet(
            total_packages = 6,
        )
    ),
    flags=[
        PackageFlag(
            code=Flag.CL,
            value=True
        )
    ],
)
# create packages
packages = [package]

# create rest_connector
rest_con = ppl.connector()

# create rest_action
response = rest_con.post_shipments(
    packages=packages,
    file_path = './out_test',
    file_name = 'test_010223.pdf',
)
```
Response from the API is a dictionary containing the following keys:
- `labels`: base64 encoded labels from the API (all together)
- `packages`: list of `Package` instances (initionaly passed to the `post_shipments` function) with extended `shipment_number` attribute, `label_base64` attribute (with single label) and extended `package_set` attribute (with `related_packages` attribute containing list of `Package` instances related to the current package with the same `reference_id` attribute but different `shipment_number` attribute)  

### Get label for a package
```python
# TODO
```


## Development
If you're keen on contributing to this project, you can do so by forking this repository and creating a pull request. Please make sure to follow the [PEP8](https://www.python.org/dev/peps/pep-0008/) style guide.