maayanlab_bioinformatics.api package

Submodules

maayanlab_bioinformatics.api.enrichr module

class maayanlab_bioinformatics.api.enrichr.EnrichrUserList(genes, description='', shortId=None, userListId=None, enrichr_link='https://maayanlab.cloud/Enrichr')[source]

Bases: object

Object oriented access to Enrichr results.

Example:

from maayanlab_bioinformatics.api import EnrichrUserList
mylist = EnrichrUserList([
  'STAT1', 'ACE2', #...
], 'mylist')
print(mylist.link)
mylist['GO_Biological_Process_2021'] # returns dataframe with enrichment results
property description
static from_url(enrichrUrl)[source]

Build object from an existing enrichr share url, e.g. userlist = EnrichrUserList.from_url(’https://maayanlab.cloud/Enrichr/enrich?dataset=285c88882ac50767f2a452c1e93632fd’)

property genes
property shortId
property userListId
maayanlab_bioinformatics.api.enrichr.enrichr_get_top_results(userListId, bg, enrichr_link='https://maayanlab.cloud/Enrichr', sleep=1)[source]

Functional access to Enrichr API

maayanlab_bioinformatics.api.enrichr.enrichr_term_genes(bg, terms, enrichr_link='https://maayanlab.cloud/Enrichr', sleep=1)[source]

maayanlab_bioinformatics.api.speedrichr module

maayanlab_bioinformatics.api.speedrichr.speedenrich(userlist: List[str], libraries: List[str] | None = None, background: List[str] | None = None, description='Example gene list', base_url='https://maayanlab.cloud/speedrichr')[source]

Perform enrichment analysis using speedrichr.

Parameters:

  • userlist – A list of genes (e.g. [‘PHF14’, ‘RBM3’, ‘MSL1’, …])

  • libraries – One or more Enrichr Libraries (https://maayanlab.cloud/Enrichr/#libraries) (e.g. [“TRANSFAC_and_JASPAR_PWMs”])

  • background – An optional background geneset for background correction (e.g. [‘PHF14’, ‘RBM3’, ‘MSL1’, …])

  • base_url – If using a different enrichr instance than the public one, specify the base prefix

Returns:

A pandas dataframe with enrichment results

Module contents

This module contains API wrappers for some commonly used tool APIs