Alternatives and similar repositories for flexynesis

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

• epigen / CellWhisperer
  CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets
  ☆187Updated last month
• bowang-lab / IntegrAO
  Integrate Any Omics: Towards genome-wide data integration for patient stratification
  ☆58Updated 8 months ago
• BIMSBbioinfo / VoltRon
  Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
  ☆116Updated 3 weeks ago
• ruppinlab / PERCEPTION
  Utilizing single-cell omics from patients tumor to predict response and resistance.
  ☆71Updated 2 years ago
• DanHanh / scLinear
  ☆19Updated last year
• czbiohub-sf / tabula-muris-senis
  Tabula Muris Senis
  ☆108Updated 2 years ago
• ArcInstitute / SRAgent
  LLM agents for working with the SRA and associated bioinformatics databases.
  ☆149Updated 2 months ago
• BIMSBbioinfo / compgen_course_2025_module3
  Compgen Course 2025, Module 3 Course Material, Multi-omics integration using deep learning
  ☆64Updated 6 months ago
• Novartis / DRUG-seq
  DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline
  ☆34Updated 10 months ago
• czi-ai / transcriptformer
  ☆100Updated 3 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆161Updated 2 weeks ago
• saezlab / corneto
  Unified knowledge-driven network inference from omics data
  ☆91Updated this week
• cantinilab / scPRINT
  🏃 The go-to single-cell Foundation Model
  ☆138Updated last month
• KrishnaswamyLab / SingleCellWorkshop
  ☆96Updated 5 years ago
• snap-stanford / SATURN
  ☆156Updated last year
• GPTomics / bioSkills
  a set of SKILLS.md for doing bioinformatics with agents like claude code
  ☆200Updated this week
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆62Updated last week
• Trhova / Multi-omics
  Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique s…
  ☆75Updated last month
• ZhangLabGT / scMultiSim
  A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
  ☆69Updated 3 months ago
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆84Updated 4 years ago
• broadinstitute / depmap_omics
  What you need to process the Quarterly DepMap-Omics releases from Terra
  ☆125Updated this week
• MaayanLab / blitzgsea
  Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for …
  ☆59Updated 8 months ago
• immunitastx / coding_exercise_TCGA_infiltration
  coding exercise using TCGA immune infiltration data
  ☆46Updated 2 years ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆149Updated 3 years ago
• DendrouLab / panpipes
  Multi-modal single cell analysis pipelines
  ☆62Updated 2 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆117Updated 3 weeks ago
• rezacsedu / XAI-for-bioinformatics
  Explainable AI for Bioinformatics
  ☆127Updated 2 years ago
• saezlab / pypath
  Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotat…
  ☆157Updated 2 weeks ago
• bedapub / besca
  BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
  ☆50Updated 8 months ago
• ncbi-nlp / GeneAgent
  The code for gene set analysis by accessing domain databases
  ☆97Updated last month