Seurat meets tidyverse. The best of both worlds.

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

R package for pre-processing of mass and flow cytometry data

PlotTwist - a web app for plotting and annotating time-series data

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

This package has migrated to https://github.com/rezakj/iCellR please use iCellR instead of scSeqR for more functionalities and updates.

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices

Tools for Batch Effects Diagnostics and Correction

Normalization for single cell RNA-seq data

LambertW R package: Lambert W x F distributions and Gaussianization for skewed & heavy-tailed data

Archived version of RUVSeq

Cytofin-an R package for CyTOF data integration

'geoquimica' is an open-source package built-in ≥ R 3.6.0 that gathers functions for assist on the exploration data analysis of geochemistry data. This package was built by researchers of the Geological Survey of Brazil.

An archived version of the scran repository, see https://github.com/MarioniLab/scran for the active version.

MUREN: a Robust and Multi-reference Approach of RNA-seq Transcript Normalization

Methylation array preprocessing.

R package: Condition-Decomposition Normalization for Biological Applications

Detecting hidden batch factors through data adaptive adjustment for biological effects