semvec/pypi-packages huggingface dataset:
Spanve 0.1.6
Spatial Neighborhood Variably Expressed Genes (Spanve) is a method for detecting spatial variably expressed genes in spatial transcriptomics data.

# Spanve: A Statistical Method for Detecting Downstream-friendly Spatially Variable Genes in Large-scale Spatial Transcriptomics Data

## Citation
```
@preprint{b.23.SpanveStatistical,
  title = {Spanve: An {{Statistical Method}} to {{Detect Clustering-friendly Spatially Variable Genes}} in {{Large-scale Spatial Transcriptomics Data}}},
  author = {{Guoxin Cai} and {Yichang Chen} and {Shuqing Chen} and {Xun Gu} and {Zhan Zhou}},
  date = {2023-01-01},
  journaltitle = {bioRxiv},
  pages = {2023.02.08.527623},
  doi = {10.1101/2023.02.08.527623},
  url = {http://biorxiv.org/content/early/2023/03/08/2023.02.08.527623.abstract},
}
```

Analysis code for the paper is available at `Evaluate` directory.

## Installation

- Install by pip (recommend):

```bash
pip install Spanve
```

- no install usage:

```bash
# install required packages
cd Evaluate/Softs
pip install spanve_requirements.txt
cp Spanve.py $your_path
```

## Usage

### cli usage

```bash
spanve --help
```

```
Usage: Spanve [OPTIONS]

Options:
  -i, --input_file PATH       input anndata file(h5ad file.)
  -r, --running_mode TEXT     running mode, default is f(c:cluster;
                              i:imputation; f:fitting)
  -s, --save_path PATH        save path
  -v, --verbose BOOLEAN       verbose
  -n, --njobs INTEGER
  -p, --preprocessed BOOLEAN  int preprocessed or not.
  --help                      Show this message and exit.****
```
command line usage can only run in a standard h5ad file, where there is a `anndata.AnnData.obsm` key named `'spatial'`.

### python usage

#### Quick Start

```python
from Spanve import Spanve
adata = sc.read_h5ad('data.h5ad')
spanve = Spanve(adata)
# -- fitting for spatial genes
spanve.fit()
spanve.save('result.csv')
# -- spatial imputation
X = adata_preprocess(adata)
X_ = spanve.impute_from_graph(X[:,spanve.rejects])
```

#### Details

see [tutorial notebook](tutorial.ipynb) or [html page](https://github.com/gx-Cai/Spanve/wiki/Tutorial).
ifcdate 0.1.3
Convert dates between Unix, Gregorian, and International Fixed Calendar
Requires Python: >=3.8

# UnixToIFCTime

A Python script to convert Unix timestamps to the International Fixed Calendar (IFC) format and vice versa.

**Note:** This implementation deviates from the original IFC proposal by adding leap year days (Year Day and Leap Day) to the end of the year, rather than placing them within the calendar as originally suggested.

## Features

- Converts Unix timestamps to IFC dates.
- Accepts date input in `YYYY-MM-DD` format and outputs the corresponding IFC date.
- Supports leap years and special days (Leap Day, Year Day).

## Usage

```bash
python unixToIfcTime.py [-d DATE] [-u UNIXTIME]