Python

SIMBA
SIMBA ( SIngle-cell eMBedding Along with features) is a versatile single-cell embedding method that co-embeds cells and features into the same latent space. https://simba-bio.readthedocs.io
May 29, 2023
SIMBA
STREAM
STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an comprehensive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.
Jan 4, 2022
STREAM
singlecellVR
A user-friendly web application for visualizing single-cell data, designed for cheap and easily available virtual reality hardware http://www.singlecellvr.com.
Oct 31, 2021
singlecellVR
scvr
scvr enables the conversion of standard outputs from commonly-used single-cell analysis tools to singlecellVR-compatible objects.
Mar 25, 2021
STREAM website
An interactive website for STREAM http://stream.pinellolab.org
Oct 23, 2020
STREAM ATACseq
A STREAM companion package for single cell ATAC-seq preprocessing
Dec 11, 2019
GiniClust
GiniClust is a clustering method implemented in Python and R for detecting rare cell-types from large-scale single-cell gene expression data.
Jun 18, 2018
GiniClust
MEGATRON (coming soon)
MEGA TRajectories of clONes.
Jan 1, 0001
STREAM2 (coming soon)
Fast, scalable, and interactive trajectory analysis of single-cell omics data.
Jan 1, 0001