vivekkohar

destiny

R package for single cell and other data analysis using diffusion maps

mousegwas

An R package for easy execution of mouse GWAS

networkx

Official NetworkX source code repository.

nextflow-starter-cloud

nonlinearTseries

Nonlinear time series analysis in R

sRACIPE

sRACIPE for bioconductor

odeint-v2

odeint - solving ordinary differential equations in c++ v2

PanglaoDB

metadata and data from the database

PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

PoincareMaps

The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

seurat

R toolkit for single cell genomics

SJARACNe

Scalable Tool for Gene Network Reverse Engineering

test

tinytest

A lightweight, no-dependency, but full-featured package for unit testing in R

visNetwork

R package, using vis.js library for network visualization

vivekkohar.github.io

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