cole-trapnell-lab/monocle3

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Updated 3 months ago

cole-trapnell-lab/monocle3

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MONOCLE 3

Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments. To use this package, you will need the R statistical computing environment (version 3.0 or later) and several packages available through Bioconductor and CRAN.

Details on how to install and use Monocle 3 are available on our website:

http://cole-trapnell-lab.github.io/monocle3/

cufflinks

monocle-release

garnett

Automated cell type classification

cicero-release

sci-plex

repository containing analysis scripts and auxiliary files

monocle2-rge-paper

Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)

Jupyter Notebook

Scribe

Regulatory networks with Direct Information

cole-trapnell-lab.github.io

leidenbase

worm-rna

The C. elegans transcriptome at single cell resolution

Jupyter Notebook

pseudospace

cicero

yeast_umap

Using UMAP on gene expression data from single-gene deletion strains of yeast to identify gene interactions

scRNASeqSim

A simulator for measuring developmental trajectories with single-cell RNA-seq

hooke

A package for comparing cell type abundances between conditions

DDRTree

An R implementation of the DDRTree algorithm for learning principal graphs

HSMMSingleCell

sci-Plex-GxE

Repository of analysis code for sci-Plex-GxE analysis

sci-Space

Contains all the code used in the analysis of the sci-Space paper

monocle

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/monocle.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=monocle.

sdg-zfish

rccm

A modified cross-convergence mapping library