Repositories list

• genbait

  Public
  GENBAIT: Genetic Algorithm for Bait Selection

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• 2023-cytomarkerpaper-analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• starling

  Public
  Segmentation error aware clustering for multiplexed imaging

  Python

  •

  Other

  •2•12•7•6•Updated Oct 24, 2024Oct 24, 2024

• cytomarker

  Public
  Interactive design and validation of antibody panels using single-cell atlases

  R

  •

  Other

  •0•2•4•0•Updated Oct 16, 2024Oct 16, 2024

• genbait_reproducibility

  Public
  GENBAIT Reproducibility

  Python

  •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• PDAC_cellular_niche_analyses

  Public
  Code implementing the analysis workflow and the probabilistic model for decoding multicellular niches in PDAC

  R

  •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

• astir

  Public
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨

  machine-learningmultiplexed-imagingimaging-mass-cytometry

  Python

  •

  GNU General Public License v2.0

  •11•51•6•9•Updated Jun 6, 2024Jun 6, 2024

• beyond_benchmarking_analyses

  Public
  R

  •

  GNU General Public License v3.0

  •0•7•1•0•Updated May 31, 2024May 31, 2024

• ACB_I_II

  Public
  JavaScript

  •0•0•0•0•Updated May 16, 2024May 16, 2024

• rdrop2

  Public
  Dropbox Interface from R

  R

  •

  Other

  •59•0•0•0•Updated Mar 25, 2024Mar 25, 2024

• active-learning-benchmarking

  Public
  R

  •0•3•0•0•Updated Dec 18, 2023Dec 18, 2023

• active-learning-benchmarking-archive

  Public
  R

  •0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

• HEB_RNASeq

  Public
  R

  •0•0•0•0•Updated Sep 21, 2023Sep 21, 2023

• scvi-tools-skeleton

  Public template
  Template repository for creating novel models with scvi-tools

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •7•0•0•1•Updated Jun 5, 2023Jun 5, 2023

• 2022_manatee_paper_analyses

  Public
  Code implementing MANATEE used for the analyses in the associated paper.

  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated May 30, 2023May 30, 2023

• leader

  Public
  R

  •0•2•0•0•Updated May 30, 2023May 30, 2023

• 2021_SCVAR

  Public
  Python

  •0•1•0•0•Updated Apr 4, 2023Apr 4, 2023

• infercnv-snakemake

  Public
  R

  •0•0•1•0•Updated Mar 3, 2023Mar 3, 2023

• inferorg

  Public
  inferorg: automatic inference and conversion of gene ID formats across organisms

  R

  •0•1•0•0•Updated Feb 13, 2022Feb 13, 2022

• acdc

  Public
  Bug fixed version of acdc

  Python

  •1•1•0•0•Updated Aug 3, 2021Aug 3, 2021

• taproom

  Public
  taproom: Tools for spAtial PROteOmics | 🍻 🖥

  R

  •

  Other

  •0•0•0•0•Updated Aug 3, 2021Aug 3, 2021

• astir-manuscript

  Public
  Analysis code for "Automated assignment of cell identity from single-cellmultiplexed imaging and proteomic data"

  R

  •0•1•1•0•Updated Aug 3, 2021Aug 3, 2021

• AstirRuntime

  Public
  Python

  •0•0•0•0•Updated Jul 29, 2021Jul 29, 2021

• Astir-Vignette

  Public
  Jupyter Notebook

  •0•3•0•0•Updated Jun 18, 2021Jun 18, 2021

• schapiro-2017

  Public
  Pipeline to process tiff files + masks from Schapiro 2017 https://pubmed.ncbi.nlm.nih.gov/28783155/

  Python

  •0•1•0•0•Updated Jan 26, 2021Jan 26, 2021

• margo

  Public
  Generates cell type marker which could be used for astir classification.

  bioinformatics

  Python

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Sep 9, 2020Sep 9, 2020

• VAE-project-JH

  Public
  Python

  •0•0•0•0•Updated Jun 9, 2020Jun 9, 2020

• cancersea

  Public
  a simple R data package for curated cancer pathway-specific gene lists

  R

  •3•8•0•0•Updated Mar 31, 2020Mar 31, 2020