emdann

milopy

Python implementation of Milo for differential abundance testing on KNN graph

ST_simulation

momicsTools

A collection of resources and knowledge for analysis of scATAC+scRNA multi omics data

sc_target_evidence

Meta-analysis of drug target evidence in single-cell data

scATAC_prep

A not-too-orderly collection of scripts for preprocessing and dimensionality reduction of scATAC-seq data

multiOmic_benchmark

Comparison of multi-omic integration methods for single-cell data.

systems-bio-sc-multiomics-2022

Materials for EBI Systems Biology course

cellatacUtils

R package for handling cellatac pipeline output

HexamerBias

Random hexamer bias analysis

multisample-sc-analysis

An overview of datasets and tools for multi-condition single-cell analysis

scanpy_hacks

starters

Computational setup checklist for new starters

bioframe

Pandas utilities for tab-delimited and other genomic data files

cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

cookiecutter-scverse

Cookiecutter template for scverse

emdann.github.io

Personal website

friendly-collab-party

Testing github

friendly-collab-party-1

testing GitHub

hexamerModel

kbroman.github.io

Karl Broman's website

ncem

Learning cell communication from spatial graphs of cells

paperpile2remarkable

Script to automate reading and annotating papers from Paperpile library on ReMarkable tablet

pertpy

Perturbation Analysis in the scverse ecosystem.

pertpy-tutorials

pypictionary

Interactive python notebook to play pictionary

scverse-tutorials

Tutorials for learning scverse

sfaira-data-curator

Scripts to curate local data stored in h5ad format

SingleCellOpenProblems

Formalizing and benchmarking open problems in single-cell genomics

SnapATAC

Single Nucleus Analysis Pipeline for ATAC-seq

trajectorama

Multi-study integration of cellular trajectories