Alternatives and similar repositories for openproblems-v2

Users that are interested in openproblems-v2 are comparing it to the libraries listed below

• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆68Updated last week
• theislab / DRVI
  Unsupervised Deep Disentangled Representation of Single-Cell Omics
  ☆48Updated this week
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆109Updated this week
• nitzanlab / biolord
  ☆81Updated last year
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆173Updated last year
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆103Updated 5 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 10 months ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆140Updated 6 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆137Updated 2 years ago
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆90Updated 3 weeks ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 6 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 4 months ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆113Updated last year
• cantinilab / scPRINT
  single cell foundation model
  ☆100Updated this week
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆166Updated 5 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆46Updated this week
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆69Updated 2 years ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆45Updated 4 years ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆66Updated 2 years ago
• theislab / scTab
  ☆59Updated 11 months ago
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆63Updated last year
• lilab-bcb / harmony-pytorch
  ☆55Updated 3 months ago
• const-ae / linear_perturbation_prediction-Paper
  ☆48Updated last month
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 7 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆198Updated this week
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆48Updated 7 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆121Updated last week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆162Updated 3 years ago
• shuxiaoc / maxfuse
  ☆55Updated last year