Alternatives and similar repositories for bicycle:

Users that are interested in bicycle are comparing it to the libraries listed below

• cantinilab / Mowgli
  Single-cell multi-omics integration using Optimal Transport
  ☆42Updated 6 months ago
• krassowski / gsea-api
  Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)
  ☆14Updated last year
• theislab / prophet
  ☆29Updated last week
• cantinilab / OT-scOmics
  This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in…
  ☆38Updated 2 years ago
• Genentech / sVAE
  ☆59Updated last year
• theislab / graphcompass
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
  ☆35Updated 2 months ago
• pachterlab / picasso
  Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.
  ☆70Updated 8 months ago
• PayamDiba / SERGIO
  A simulator for single-cell expression data guided by gene regulatory networks
  ☆59Updated 10 months ago
• mims-harvard / PDGrapher
  Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks
  ☆23Updated 3 months ago
• bowang-lab / BIONIC
  Biological Network Integration using Convolutions
  ☆62Updated last year
• TuftsBCB / RegDiffusion
  Diffusion model for gene regulatory network inference.
  ☆16Updated last week
• sanderlab / CellBox
  CellBox: Interpretable Machine Learning for Perturbation Biology
  ☆53Updated last year
• msmdev / pyGPCCA
  pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state mo…
  ☆21Updated 3 months ago
• jmschrei / ledidi
  Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
  ☆71Updated 2 months ago
• labsyspharm / visinity
  ☆16Updated 9 months ago
• sunericd / TISSUE
  TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) provides tools for estimating well-calibrated uncertainty …
  ☆29Updated last year
• causalbench / causalbench-starter
  Starter repository for submissions to the CausalBench challenge for gene-gene graph inference from genetic perturbation experiments.
  ☆29Updated last year
• saezlab / corneto
  Unified knowledge-driven network inference from omics data
  ☆32Updated last week
• cbg-ethz / scDEF
  Deep exponential families for single-cell data.
  ☆21Updated 4 months ago
• dynverse / dyngen
  Simulating single-cell data using gene regulatory networks 📠
  ☆74Updated last year
• krishnanlab / obnb
  A Python toolkit for setting up benchmarking dataset using biomedical networks
  ☆22Updated this week
• PathwayAndDataAnalysis / causalpath
  A project for exploring differentially active signaling paths related to proteomics datasets
  ☆40Updated 5 months ago
• KrishnaswamyLab / Multiscale_PHATE
  Creating multi-resolution embeddings and clusters from high dimensional data
  ☆52Updated 6 months ago
• krishnanlab / PyGenePlexus
  A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input ge…
  ☆20Updated this week
• theislab / ncem
  Learning cell communication from spatial graphs of cells
  ☆108Updated last year
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆55Updated last year
• shangll123 / SpatialPCA
  Spatially aware dimension reduction for spatial transcriptomics.
  ☆46Updated last week
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆39Updated 10 months ago
• cantinilab / scPRINT
  single cell foundation model for Gene network inference and more
  ☆57Updated this week
• menchelab / CartoGRAPHs
  ☆23Updated 10 months ago