paularstrpo

sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

anndata2ri

Convert between AnnData and SingleCellExperiment

SPATA2

A Toolbox for Spatial Expression Analysis

tidySpatialExperiment

SpatialExperiment with tidy principles

tidySingleCellExperiment

Brings SingleCellExperiment objects to the tidyverse

tidyseurat

Seurat meets tidyverse. The best of both worlds.

SpatialDE

Test genes for Spatial Variation

SpatialDE

Test genes for Spatial Variation

SpatialExperiment

persist

globus-flows-trigger-examples

Sample code for triggering Globus Flows using the Python watchdog library.

seurat-disk

Interfaces for HDF5-based Single Cell File Formats

openmoji

Open source emojis for designers, developers and everyone else!

NicheDE

NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.

vizgen-postprocessing

scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

spatialbenchmark_reproducibility

CellSPA

Cell Segmentation Performance Assessment

BIDCell

Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

seurat-wrappers

Community-provided extensions to Seurat

ROGUE

Assessing the purity of single cell population

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

ALRA

Imputation method for scRNA-seq based on low-rank approximation

STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

ncem

Learning cell communication from spatial graphs of cells

ncem_tutorials