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scCalibratoR

scCalibratoR is a Bioconductor package designed to streamline the process of aligning single-cell RNA sequencing (scRNA-seq) datasets from different batches or sources. It also provides tools for identifying and correcting potential misannotations in cell populations by highlighting the genes responsible for discrepancies.

Features

  • Batch Effect Correction: Align single-cell datasets to a trusted reference dataset, mitigating technical noise while preserving biological signals.
  • Annotation Refinement: Detect and correct potentially misannotated cells by comparing gene expression profiles to reference profiles.
  • Gene Driver Identification: Identify specific genes driving annotation discrepancies, facilitating targeted corrections.
  • Visualization and Reporting: Generate visualizations and reports to summarize alignment and correction processes, aiding in interpretation and validation.

Installation

To install the development version of the package from GitHub use the following command:

BiocManager::install("ccb-hms/scCalibratoR")

NOTE: you will need the BiocManager package to install from Bioconductor.

To build the package vignettes upon installation use:

BiocManager::install("ccb-hms/scCalibratoR",
                     build_vignettes = TRUE,
                     dependencies = TRUE)