--- a +++ b/docs/source/pycombat.rst @@ -0,0 +1,39 @@ +============================= +Batch Effect Correction Tools +============================= + +Variability in datasets not only results from biological processes, but also +from technical bias [Lander1999]_. +InMoose offers a collection of tools for the correction of such technical bias, +also called batch effects. + +Please refer to [Behdenna2023]_ for a detailed comparison of InMoose +implementation with the original R implementations. + +.. toctree:: + :maxdepth: 1 + :caption: Batch effect correction per type of data: + + for microarray data <pycombatnorm> + for RNASeq data <pycombatseq> + + +References +========== + +.. [Behdenna2023] A. Behdenna, M. Colange, J. Haziza, A. Gema, G. Appé, C.-A. + Azencott and A. Nordor. 2023. pyComBat, a Python tool for batch effects + correction in high-throughput molecular data using empirical Bayes methods. + *BMC Bioinformatics* 7;24(1):459. :doi:`10.1186/s12859-023-05578-5` + +.. [Johnson2007] W. E. Johnson, C. Li, A. Rabinovic. 2007. Adjusting batch + effects in microarray expression data using empirical Bayes methods. + *Biostatistics*, 8, 118–12. :doi:`10.1093/biostatistics/kxj037` + +.. [Lander1999] E. S. Lander. 1999. Array of hope. *Nature Genetics*, 21(1 + Suppl), 3-4. :doi:`10.1038/4427` + +.. [Zhang2020] Y. Zhang, G. Parmigiani, W. E. Johnson. 2020. ComBat-Seq: batch + effect adjustment for RNASeq count data. *NAR Genomics and Bioinformatics*, + 2(3). :doi:`10.1093/nargab/lqaa078` +