deevdevil88

MedSAM

Segment Anything in Medical Images

singleCellTK

Interactively analyze single cell genomic data

glasbey

Algorithmically create or extend categorical colour palettes

SATURN

scimilarity

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

airrflow

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

zero-shot-scfoundation

PINNACLE

Contextualizing protein representations using deep learning on protein networks and single-cell data

midas

cytomapper

R package for visualization of highly multiplexed imaging data

shannonca

Information-based dimensionality reduction

CytoCommunity

The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains

PCAtest

R package PCAtest for evaluating the statistical significance of PCA analysis, selecting number of significant PC axes, and testing the contributions of the variables to those PCs.

decipher

A single-cell analysis toolkit to jointly analyze samples from distinct conditions

velocycle

Bayesian model for RNA velocity estimation of periodic manifolds

DSPIN

Code and example of the D-SPIN framework

scDrugPrio

Network analyses of single cell-based digital twins for personalized treatment of inflammatory disease

TissueTag

Python package to interactively annotate histological images within a jupyter notebook

SingleCellAlleleExperiment

implementation of a single cell allele experiment object

resimpy

Simulating reads of varying sequencing technologies

TallyTriN

Repo for working on long-read triple amidite bulk RNA-seq

cellphonedbviz

Interactive visualisation of CellphoneDB results

hooke

A package for comparing cell type abundances between conditions

GeNA

Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets

DeconvoBuddies

Helper Functions for LIBD Deconvolution

multi-condition-comparisions

Functions for analyzing and visualizing multi-condition single-cell data (prototypes created at Cambridge hackathon)

HRCA-reproducibility

Scripts related to the Human Retina Cell Atlas (Chen / Theis labs).

VIVS

Calibrated Identification of Feature Dependencies in Single-cell Multiomics

proust

Proust: graph-based using spatially resolved transcriptomics and immunofluorescence images

proust_paper

Figures and resutls for Proust