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gpseudotime

Bayesian Gaussian Process Latent Variable Models for pseudotime inference in single-cell RNA-seq data

gpy

Gaussian processes framework in python

hello-github-actions

helmholtz

Helmholtz-Hodge decomposition using fft

hl60-tf-model_v4

Fourth generation HL60 TF model w/the Adjoint system of equations

hodge-graphs

Some fun with combinatorial Hodge decompositions from graphs.

hodge.jl

Cochains over Simplicial Complexes, including their Hodge decomposition.

irlba

Fast truncated singular value decompositions

jungle

jungle

kneed

Knee point detection in Python :chart_with_upwards_trend:

mast

Tools and methods for analysis of single cell assay data in R

matplotlib

matplotlib: plotting with Python

ml-visuals

🎨 ML Visuals contains figures and templates which you can reuse and customize to improve your scientific writing.

mmpca

R package for mixture of multinomial PCA

multispatialccm

Multispatial Convergent Cross Mapping

multiview

mxnet

Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Go, Javascript and more

nbt_spatial_backmapping

code source for the manuscript: Single-cell expression profiling and spatial mapping into tissue of origin

netgraph

Drawing utilities for publication quality plots of networks

nmslib

Non-Metric Space Library (NMSLIB): A similarity search library and a toolkit for evaluation of k-NN methods for generic non-metric spaces.

paper-data

pciseq

A probabilistic cell typing algorithm for spatial transcriptomics.

perturbseq_demo

Tutorial for using the perturbseq library to load and manipulate experiments

perturbseq_gi

Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"

potree

WebGL point cloud viewer for large datasets

pydstool

PyDSTool main development repo

pynamical

Pynamical is a Python package for modeling and visualizing discrete nonlinear dynamical systems, chaos, and fractals.

pyopenworm

Unified, simple data access python library for data & facts about C. elegans anatomy

pysd

System Dynamics Modeling in Python

pysmfish

Analysis of smFISH data