PauBadiaM

followers

following

stars

Heidelberg University

Heidelberg, Deutschland

Pau Badia i Mompel's starred repositories

pyranges

Performant Pythonic GenomicRanges

Language:PythonMIT41500

SnapATAC2

Single-cell epigenomics analysis tools

Language:Python18300

marsilea

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

Language:PythonMIT5000

anndata

Annotated data.

Language:PythonBSD-3-Clause50900

pychromVAR

A python package for chromVAR

Language:PythonMIT2100

corneto

CORNETO: A Unified Omics-Driven Framework for Network Inference

Language:PythonGPL-3.01300

slurm

Cookiecutter for snakemake slurm profile

Language:PythonMIT12200

scMEGA

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

Language:RNOASSERTION3200

sc-SHC

Significance analysis for clustering single-cell RNA-sequencing data

Language:HTML8500

PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

Language:PythonMIT23700

PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)

Language:Jupyter NotebookMIT19000

HuMMuS

Molecular interactions inference from single-cell multi-omics data

Language:PythonAGPL-3.01400

CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions

Language:RGPL-3.04300

HiC_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

MIT15500

PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Language:PythonMIT52800

biocypher

A unifying framework for biomedical research knowledge graphs

Language:PythonMIT19100

single-cell-best-practices

https://www.sc-best-practices.org

Language:Jupyter NotebookNOASSERTION66600

FigR

Functional Inference of Gene Regulation

Language:HTMLMIT3000

scMultiSim

A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.

Language:R1800

EUGENe

Elucidating the Utility of Genomic Elements with Neural Nets

Language:Jupyter NotebookMIT5900

liana-py

LIANA+: an all-in-one framework for cell-cell communication

Language:PythonGPL-3.012100

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

Language:PythonAGPL-3.010000

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

Language:PythonGPL-3.017800

mistyR

Multiview Intercellular SpaTial modeling framework

Language:RGPL-3.03900

Pando

Multiome GRN inference.

Language:RMIT10200

muon

muon is a multimodal omics Python framework

Language:PythonBSD-3-Clause20000

dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Language:PythonBSD-3-Clause40500

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language:PythonBSD-3-Clause114300

datasets

🤗 The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools

Language:PythonApache-2.01858800

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

Language:PythonApache-2.028200