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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.
Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
This package has migrated to https://github.com/rezakj/iCellR please use iCellR instead of scSeqR for more functionalities and updates.
Tools for Batch Effects Diagnostics and Correction
LambertW R package: Lambert W x F distributions and Gaussianization for skewed & heavy-tailed data
Cytofin-an R package for CyTOF data integration
Archived version of RUVSeq
'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.
Methylation array preprocessing.
An archived version of the scran repository, see https://github.com/MarioniLab/scran for the active version.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
R package: Condition-Decomposition Normalization for Biological Applications
Detecting hidden batch factors through data adaptive adjustment for biological effects