Welcome to eco_helper’s documentation!

eco_helper is a command line toolbox for data preprocessing to automate common tasks. eco_helper was specifically designed to automate pre-processing tasks related to working with the EcoTyper framework for transcriptomics data. However, the tasks performed by eco_helper can be used for other purposes as well. While designed primarily as a command line tool, eco_helper is also a Python package and can be used directly within python scripts. In fact, some few functionalities of eco_helper can only be accessed via the code API and not via command line. These are minor functions, however, such as passing kwargs to file-reading functions, and does not impact the usability from command line in most cases.

There are five primary commands offered by eco_helper:

>>> eco_helper convert

The convert command is used to convert data from one format to another. Supported formats are tabular formats such as TSV, Matrix Transfer Archive (mtx), and SeuratObjects stored in RDS files.

>>> eco_helper normalise

The normalise command is used to normalise data to TPM or CPM.

>>> eco_helper format

The format command is used to reformat data columns and headers from a tabular file. The purpose of this is to eliminate invalid characters for downstream software. For instance, EcoTyper does not accept spaces or minuses in the column headers or index. Therefore, using this command one can replace automatically such characters (or any other regex pattern).

>>> eco_helper enrich

The enrich command is used to perform gene set enrichment analysis on EcoTyper results using the gseapy package. This allows automated gene set enrichment analysis using either enrichr or prerank gseapy analyses directly on all cell types and their identified cell states.

>>> eco_helper drop

The drop command is used to drop remove entries from ecotyper datasets. Specific entries, entire celltypes, or samples can be removed.

Contents:

• Filetype Conversion
  • Usage
  • Full CLI
  • eco_helper.convert.funcs module
  • eco_helper.convert.tabular module
  • eco_helper.convert.mtx module
  • eco_helper.convert.seurat module
• Data Normalisation
  • Usage
  • Full CLI
  • eco_helper.normalise.NormTable module
  • eco_helper.normalise.funcs module
• Data Re-Formatting
  • Usage
  • Full CLI
  • eco_helper.format.Formatter module
  • eco_helper.format.funcs module
  • eco_helper.format.Pseudo module
  • eco_helper.format.formats
• Gene Set Enrichment Analysis
  • Usage
  • Full CLI
  • Web-Viewer
  • Jupyter Notebook
  • eco_helper.enrich.funcs module
  • eco_helper.enrich.visualise module
• Core Functions
  • eco_helper.core.CellTypeCollection
  • eco_helper.core.CellStateCollection
  • eco_helper.core.EcoTypeCollection
  • eco_helper.core.gene_sets module
  • eco_helper.core.EcoTyperConfig
  • eco_helper.core.Dataset
  • eco_helper.core settings
  • eco_helper.core.terminal_funcs module
  • eco_helper.core.TerminalOutput
  • eco_helper.core.find module

Indices and tables

• Index

• Module Index

• Search Page

  Short disclaimer on the logo: The logo is, obiously, a derivative of the original EcoTyper logo. No infringement is intended, all credits go to the original designer in the EcoTyper development team.