A toolkit for navigating and analyzing gene expression datasets
Project description
# ![XPRESStools](https://raw.githubusercontent.com/XPRESSyourself/XPRESStools/master/docs/content/xpresstools.png)
### A toolkit for navigating and analyzing gene expression datasets
[![Build Status](https://travis-ci.org/XPRESSyourself/XPRESStools.svg?branch=master)](https://travis-ci.org/XPRESSyourself/XPRESStools)
[![Documentation Status](https://readthedocs.org/projects/xpresstools/badge/?version=latest)](https://xpresstools.readthedocs.io/en/latest/?badge=latest)
[![PyPi Status](https://img.shields.io/pypi/v/XPRESStools.svg)](https://pypi.org/project/XPRESStools/)
##### Find documentation [here](https://xpressyourself.github.io/XPRESStools/)
-----
### Development Notes:
<b><i>XPRESStools is still in beta production</i></b>
### Citation:
```
Berg, JA (2019). XPRESSyourself suite: Gene expression processing and analysis made easy. https://github.com/XPRESSyourself.
```
### Installation:
```
conda install -c bioconda xpresstools
```
### QuickStart:
```
>>> import pandas as pd
>>> import xpresstools as xp
>>> geo, metadata = xp.get_geo('GSE20916')
>>> geo = xp.rpm(geo)
```
### Important Notes:
Assumes all dataframes are columns=samples and rows=genes (except in certain cases, see documentation for help)
```
>>> geo.head()
name GSM523242 GSM523243 GSM523244 GSM523245 GSM523246 GSM523247 ...
1007_s_at 8.98104 8.59941 8.25395 8.72981 8.70794 8.10693 ...
1053_at 5.84313 6.59168 8.27881 6.64005 4.65107 7.19090 ...
121_at 6.17189 5.73603 5.55673 5.69374 6.77618 5.84524 ...
1294_at 6.97009 6.80003 5.56620 7.43816 7.36375 5.85687 ...
1405_i_at 10.24611 10.13807 8.84743 9.72365 10.42940 9.17510 ...
[5 rows x 145 columns]
```
### A toolkit for navigating and analyzing gene expression datasets
[![Build Status](https://travis-ci.org/XPRESSyourself/XPRESStools.svg?branch=master)](https://travis-ci.org/XPRESSyourself/XPRESStools)
[![Documentation Status](https://readthedocs.org/projects/xpresstools/badge/?version=latest)](https://xpresstools.readthedocs.io/en/latest/?badge=latest)
[![PyPi Status](https://img.shields.io/pypi/v/XPRESStools.svg)](https://pypi.org/project/XPRESStools/)
##### Find documentation [here](https://xpressyourself.github.io/XPRESStools/)
-----
### Development Notes:
<b><i>XPRESStools is still in beta production</i></b>
### Citation:
```
Berg, JA (2019). XPRESSyourself suite: Gene expression processing and analysis made easy. https://github.com/XPRESSyourself.
```
### Installation:
```
conda install -c bioconda xpresstools
```
### QuickStart:
```
>>> import pandas as pd
>>> import xpresstools as xp
>>> geo, metadata = xp.get_geo('GSE20916')
>>> geo = xp.rpm(geo)
```
### Important Notes:
Assumes all dataframes are columns=samples and rows=genes (except in certain cases, see documentation for help)
```
>>> geo.head()
name GSM523242 GSM523243 GSM523244 GSM523245 GSM523246 GSM523247 ...
1007_s_at 8.98104 8.59941 8.25395 8.72981 8.70794 8.10693 ...
1053_at 5.84313 6.59168 8.27881 6.64005 4.65107 7.19090 ...
121_at 6.17189 5.73603 5.55673 5.69374 6.77618 5.84524 ...
1294_at 6.97009 6.80003 5.56620 7.43816 7.36375 5.85687 ...
1405_i_at 10.24611 10.13807 8.84743 9.72365 10.42940 9.17510 ...
[5 rows x 145 columns]
```
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