rikenbit/FUCHIKOMA: Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data

fuchikoma detects differentially expressed genes (DEGs) in one of multiple clusters. To detect DEGs, fuchikoma has two calculation mode; "supervised-mode" and "unsupervised-mode". In supervised-mode, fuchikoma detects DEGs by using a label vector, in which the cluster of each sample or cell is written. In unsupervised-mode, fuchikoma detects DEGs without the label vector. In this mode, user run the diffusion map, and specify which diffusion components contribute to the difference of such cluster.

Getting started

Package details

AuthorKoki Tsuyuzaki, Haruka Ozaki, Mika Yoshimura, Itoshi Nikaido
Bioconductor views Bioinformatics Clustering DifferentialExpression HighThroughputSequencing MultipleComparisons RNAseq Sequencing Software
MaintainerKoki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
rikenbit/FUCHIKOMA documentation built on May 27, 2019, 9:09 a.m.