batch-effect

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

UniFORM: Towards Universal ImmunoFluorescence Normalization for Multiplex Tissue Imaging

Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data

Identification of biased features from SVGs in spatial transcriptomics data

Batch-Effect Reduction Trees

Deep Embedding for Single-cell Clustering. This repo has no files related to github page so that users can download it quickly.

Parallel companions for five RNA-seq functions that are slow at cohort scale and have no worker argument: sva::ComBat_seq, edgeR::normLibSizes, limma::lmFit, limma::duplicateCorrelation and limma::removeBatchEffect. Each runs the original unmodified with its work split across workers and returns output identical() to the original's.

Batch-effect correction methods for MALDI-TOF spectra in clinical AMR prediction workflows

Pure-Python batch-effect harmonization toolkit validated, ported from HarmonizR

a single-cell multimodal mosaic data integration tool

Batch-resolved Treatment-associated Regulatory Networks

A lightweight, pip-installable version of FedscGen.

Reference-batch adjustment for bulk RNA-seq counts using quasi-likelihood modelling and empirical-Bayes moderation.

Benchmark honesto de descriptores de imagen para clasificar lesiones cutaneas dermatoscopicas (ISIC): 390 combinaciones descriptor x algoritmo, control del efecto de lote y validacion externa entre instituciones. AUC 0.741 fuera del archivo de entrenamiento.

MaldiSuite - a Python ecosystem for MALDI-TOF spectral processing and analysis in antimicrobial resistance research

Design-first analysis of TB transcriptomic cohorts: a published signature discriminates progressors across three cohorts, but its time gradient tracks the sampling window, not batch effects.

ComBat batch adjustment for ML pipelines with a scikit-learn-style API.