semvec/pypi-packages huggingface dataset:
malachite 2.0.12
A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene

# Malachite: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene

Researchers commonly use software, such as Toppgene and online tools to conduct enrichment analyses on gene expression data. This process does not allow multiple gene data sets to be analyzed and compared at once. Malachite allows researchers to perform enrichment analyses on multiple gene lists and concatenate the resulting enrichment statistics, thus, enabling meta-enrichment analyses across multiple data sets. Requires Windows 10, MacOS 10.11 or Linux Mint 18.

# How to Use:

## Command Line Argument Descriptions:

#### 1. Full path to input file:

ex. "/Desktop/myInput/input.xlsx"

#### 2. Input type:
###### Choose one: HGNC, HGNC_SYNONYMS, ENTREZ, ENSEMBL, REFSEQ, UNIPROT

ex. "HGNC"

#### 3. Categories:
###### Options: "GeneOntologyMolecularFunction": "GO: Molecular Function", "GeneOntologyBiologicalProcess": "GO: Biological Process", "GeneOntologyCellularComponent":"GO: Cellular Component", "HumanPheno":"Human Phenotype","MousePheno":"Mouse Phenotype","Domain":"Domain", "Pathway":"Pathway","Pubmed":"Pubmed","Interaction":"Interaction","Cytoband":"Cytoband","TFBS":"Transcription Factor Binding Site","GeneFamily":"Gene Family","Coexpression":"Coexpression","CoexpressionAtlas":"Coexpression Atlas","Computational":"Computational","MicroRNA":"MicroRNA","Drug":"Drug","Disease":"Disease"

ex. ["Drug", "Disease", "GeneOntologyMolecularFunction"]

#### 4. Individual Toppgene analyses output path:

ex. "/Desktop/Results/IndividualResults/"


#### 5. Final Concatenated Results Output path:

ex. "/Desktop/Results/ConcatenatedResults/"

# For Example,

### In terminal type...

malachite "/Desktop/myInput/input.xlsx" "HGNC" ["Drug", "Disease", "GeneOntologyMolecularFunction"] "/Desktop/Results/IndividualResults/" "/Desktop/Results/ConcatenatedResults/"

### *NOTE: quotation marks (“/‘) can be glitchy, make sure you use straight quotes, not curly quotes.
### *NOTE: input data has to be of type .xlsx
falcontyping 0.7.0
Add type hints support to Falcon with Pydantic and Marshmallow integration
Requires Python: >=3.7.0
Keywords: falcon,typing,hints,mypy,pydantic,marshmallow

# Falcon typing

![PyPI - Python Version](https://img.shields.io/pypi/pyversions/falcontyping)
![PyPI](https://img.shields.io/pypi/v/falcontyping)
[![codecov](https://codecov.io/gh/abdelrahman-t/falcontyping/branch/master/graph/badge.svg)](https://codecov.io/gh/abdelrahman-t/falcontyping)
[![Build Status](https://travis-ci.org/abdelrahman-t/falcontyping.svg?branch=master)](https://travis-ci.org/abdelrahman-t/falcontyping)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

### Use type hints to specify request parameters with Marshmallow and Pydantic support.
**Uses [typedjson](https://github.com/mitsuse/typedjson-python)

### Example
```python
"""API."""
from typing import Optional, Union

from pydantic import BaseModel as PydanticModel
from falcontyping import TypedAPI, TypedResource


class UserV1(PydanticModel):

    username: str

class UserV2(PydanticModel):

    username: str
    balance: float


class UsersResource(TypedResource):

    def on_post(self, request, response, user: Union[UserV2, UserV1]) -> Union[UserV2, UserV1]:
        if isinstance(user, UserV2):
            return UserV2(username=user.username, balance=user.balance)

        else:
            return UserV1(username=user.username)

class UserDetailsResource(TypedResource):

    def on_get(self, request, response, user_id: int) -> Optional[Union[UserV2, UserV1]]:
        if user_id == 2:
            return UserV2(username='user', balance=0.0)

        if user_id == 1:
            return UserV1(username='user')

        return None

API = TypedAPI()
API.add_route('/users', UserResource())
API.add_route('/users/{user_id}', UserDetailsResource())
```

### How to install
`pip install falcontyping`