inmoose 0.1.0

InMoose: the Integrated Multi Omic Open Source Environment

InMoose

InMoose is the Integrated Multi Omic Open Source Environment. It is a collection of tools for the analysis of omic data.

Currently it focuses on transcriptomic data.

Installation

You can install InMoose directly with:

pip install inmoose

Batch Effect Correction

InMoose provides features to correct technical biases, also called batch effects, in transcriptomic data:

• for microarray data, InMoose supersedes pyCombat [1], a Python 3 implementation of ComBat [2], one of the most widely used tool for batch effect correction on microarray data.
• for RNASeq, InMoose features a port to Python3 of ComBat-Seq [3], one the most widely used tool for batch effect correction on RNASeq data.

To use these functions, simply import them and call them with default parameters:

from inmoose.batch import pycombat, pycombat_seq

microarray_corrected = pycombat(microarray_data, microarray_batches)
rnaseq_corrected = pycombat_seq(rnaseq_data, rnaseq_batches)

• microarray_data, rnaseq_data: the expression matrices, containing the information about the gene expression (rows) for each sample (columns).
• microarray_batches, rnaseq_batches: list of batch indices, describing the batch for each sample. The list of batches should contain as many elements as the number of samples in the expression matrix.

How to contribute

Please refer to CONTRIBUTING.md to learn more about the contribution guidelines.

References

[1] Behdenna A, Haziza J, Azencot CA and Nordor A. (2020) pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods. bioRxiv. https://doi.org/10.1101/2020.03.17.995431

[2] Johnson W E, et al. (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8, 118–12. https://doi.org/10.1093/biostatistics/kxj037

[3] Zhang Y, et al. (2020) ComBat-Seq: batch effect adjustment for RNASeq count data. NAR Genomics and Bioinformatics, 2(3). https://doi.org/10.1093/nargab/lqaa078