Skip to main content

Python Bioscience package

Project description

PyBioSci

Python BioScience is a package containing different functionalities on different BioScience algorithms. Initially the package will be focused on the Microbiome data analysis, later the functionalities will be expanded to other BioScience tasks.

Diversity Indices

This module contains different alpha and beta diversity indices to calculate the diversity of a sample and a group of samples. All the indices are discussed in this paper.

Below an example code for finding diversity indices has been shown:

from pybiosci.diversity_indicies import alpha_index 
import pandas as pd

df = pd.read_csv('data/simCounts.csv')
print(alpha_index(df, index='Shannon'))

The dataframe is expected to be in a definite format. Row represents the taxa and column represents each sample. Absolute read counts are taken as input and converted to relative abundance when required for an index. You can specify index=All to get all indices as a feature table.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pybiosci-0.0.5.tar.gz (5.9 kB view details)

Uploaded Source

Built Distribution

pybiosci-0.0.5-py3-none-any.whl (6.1 kB view details)

Uploaded Python 3

File details

Details for the file pybiosci-0.0.5.tar.gz.

File metadata

  • Download URL: pybiosci-0.0.5.tar.gz
  • Upload date:
  • Size: 5.9 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.8.10

File hashes

Hashes for pybiosci-0.0.5.tar.gz
Algorithm Hash digest
SHA256 9d474201d715409bcd6fcee10aa55068a6fd8dbeba79784349ca94f25a333081
MD5 ecfb59f2ecd11cb80e5530a15316da4d
BLAKE2b-256 96a66158533a99ccc91877f262651592eee4ceddc2b7a3b958b271bd37bd0806

See more details on using hashes here.

File details

Details for the file pybiosci-0.0.5-py3-none-any.whl.

File metadata

  • Download URL: pybiosci-0.0.5-py3-none-any.whl
  • Upload date:
  • Size: 6.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.8.10

File hashes

Hashes for pybiosci-0.0.5-py3-none-any.whl
Algorithm Hash digest
SHA256 dbdde2db8569b20544edd8abdeeae785f1bd5936fd10a1e65a666ba595d38907
MD5 564b70dc44f0d604e8cca87816d90f84
BLAKE2b-256 8f301659a0620a8b7e768a2f22d976d457045fdbe48c19006b0b3546c8082aa5

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page