A toolkit for navigating and analyzing gene expression datasets
Project description
A toolkit for navigating and analyzing gene expression datasets
Find documentation here
Development Notes:
XPRESSplot is still in beta production
XPRESSplot supports Python 2.7 and >=3.5
Citation:
Berg, JA (2019). XPRESSyourself suite: Gene expression processing and analysis made easy. https://github.com/XPRESSyourself. DOI: 10.5281/zenodo.2581692.
Installation:
pip install xpressplot
Other Requirements:
- Tested on 64-bit Linux, compatible with Mac OS X
- Python3 is recommended
- Current test cases build to:
- Python2.7
- Python3.5
- Python3.6
- Python3.7
- Current test cases build to:
- If PyPi and Conda are not already installed, these should be installed
- If using this package to perform batch effect normalization or differential expression analysis, you must install R
- If using the interactive notebook provided, Jupyter needs to be installed if not already
QuickStart:
Download the repository and modify the interactive Jupyter notebook to get started quick!
Read the instructions as you navigate through the code blocks for a guide on how to use the example code
Code blocks are run by selecting the block and pressing Shift + Enter
See documentation for more detailed instructions
Important Notes:
- If working with XPRESSplot within an interactive notebook (i.e. Jupyter Notebook, Atom Hydrogen, etc), you must include the following line of code after importing XPRESSplot
import XPRESSplot as xp
%matplotlib inline
- 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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