pymodulon.example_data

Pre-loaded example dataset for PyModulon tutorials.

Module Contents

Functions

load_ecoli_data()	Load Escherichia coli IcaData object from
load_staph_data()	Load Staphylococcus aureus IcaData object from
load_bsub_data()	Load Bacillus subtilis IcaData object from
load_example_bbh()	Load an example bi-directional blast best hit (BBH) file
load_example_log_tpm()	Load an example expression dataset in units log-TPM

Attributes

_data_dir
_ecoli_dir
M
A
X
gene_table
sample_table
imodulon_table
trn
ecoli_fasta
ecoli_gff
ecoli_eggnog
ecoli_biocyc
ecoli_go_example

pymodulon.example_data._data_dir

pymodulon.example_data._ecoli_dir

pymodulon.example_data.M

pymodulon.example_data.A

pymodulon.example_data.X

pymodulon.example_data.gene_table

pymodulon.example_data.sample_table

pymodulon.example_data.imodulon_table

pymodulon.example_data.trn

pymodulon.example_data.ecoli_fasta

pymodulon.example_data.ecoli_gff

pymodulon.example_data.ecoli_eggnog

pymodulon.example_data.ecoli_biocyc

pymodulon.example_data.ecoli_go_example

pymodulon.example_data.load_ecoli_data()

Load Escherichia coli IcaData object from [SGS+19]

Returns

ecoli_data – E. coli IcaData object

Return type

IcaData

pymodulon.example_data.load_staph_data()

Load Staphylococcus aureus IcaData object from [PTS+20]

Returns

staph_data – S. aureus IcaData object

Return type

IcaData

pymodulon.example_data.load_bsub_data()

Load Bacillus subtilis IcaData object from [RSP20]

Returns

bsub_data – B. subtilis IcaData object

Return type

IcaData

pymodulon.example_data.load_example_bbh()

Load an example bi-directional blast best hit (BBH) file

Returns

example_bbh – Example BBH file

Return type

DataFrame

pymodulon.example_data.load_example_log_tpm()

Load an example expression dataset in units log-TPM

Returns

example_tpm – Example expression dataset

Return type

DataFrame