Helmholtz Zentrum München
anndata
anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.
- bioinformatics
- data managment
- FAIR Data
- + 1
- Python
BaSiC
BaSiC is a specialized MATLAB tool designed for the background and shading correction of optical microscopy images. BaSiC addresses critical challenges in image processing, thereby enhancing the quality and reliability of microscopy data.
- MATLAB
CellRank
CellRank is a computational framework to study cellular fate decisions based on various types of single-cell genomics data. CellRank scales to large cell numbers, is fully compatible with the scverse ecosystem, and is easy to use.
- Data analysis
- fate mapping
- fate prediction
- + 7
- Python
ehrapy
ehrapy is a modular open-source Python framework designed for exploratory end-to-end analysis of heterogeneous epidemiology and electronic health record data.
- Data analysis
- open source
- python
- Python
MemBrain v2
MemBrain v2 aims to facilitate the analysis of membranes in cryo-electron tomography data. It consists of the components membrain-seg for membrane segmentation, membrain-pick for membrane protein localization, and membrain-stats for the extraction of membrane-based metrics.
- Python
scanpy
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
- bioinformatics
- Data analysis
- python
- Python
- R
scPower
scPower is a statistical framework for design and power analysis of multi-sample single cell transcriptomics experiments. It enables users to identify the optimal experimental parameters for cell type specific inter-individual DE and eQTL analysis using single cell RNA-seq data given a fixed budget.
- Experimental design
- Health
- scRNA-seq
- + 1
- R
- HTML
- CSS
SpatialData framework
SpatialData is an open and interoperable data framework for ingesting, representing, processing and visualizing spatial omics datasets.
- Data Visualization
- FAIR Data
- Multi omics
- + 3
- Python
- Dockerfile