Toolkit for Cancer Association studies.
| Name | Language | Active? | Description |
|---|---|---|---|
| TCGAbiolinks | R | Yes | An R/Bioconductor package for integrative analysis with TCGA data |
| TCGAutils | R | Yes | MultiAssayExperiment for TCGA |
| LinkedOmics | GUI |
| Name | Language | Active? | Description |
|---|---|---|---|
| ExperimentHub | R | Yes | A repository of curated biological data |
| dalmatian | Python | Yes | a collection of high-level functions for interacting with Firecloud via Pandas dataframes |
| EUGENe | Python | Yes | computational framework for machine learning based modeling of regulatory sequences |
| eugene.dataload.dataloaders.SeqData | Python | Yes | SeqData object used to containerize and store data for EUGENe workflows |
| Hail | Python | Yes | Cloud-native genomic dataframes and batch computing |
| hail.matrixtable.MatrixTable | Python | Yes | A MatrixTable is a distributed two-dimensional extension of a Table |
| HTSeq 2.0 | Python | Yes | HTSeq is a Python package for analysis of high-throughput sequencing data |
| Janggu | Python | Yes | Janggu is a python package that facilitates deep learning in the context of genomics |
| janggu.data | Python | Yes | genomics datasets maintains coverage or sequence type of information along with the associated genomic intervals. Externally, the datasets behave similar to a numpy array |
| kartothek | Python | Yes | A consistent table management library in python / manage tabular data in object stores |
| MultiAssayExperiment | R | Yes | A Bioconductor package for the representation of multi-assay experiments |
| OpenOmics | python | Yes | A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases |
| pyGeno | Python | Yes | precision medicine and proteogenomics |
| scikit-allel | Python | No | Succeeded by sgkit |
| scikit-bio | Python | Yes | mainly microbial genomics |
| scikit-genome | Python | Yes | add-on to CNVkit |
| scverse | R, Python | Yes | AnnData, muon with PyTorch for single-cell RNA-seq |
| sgkit | Python | Yes | xarray for VCFs with some statgen functionality (eg GWAS) |
| Name | Language | Active? | Description |
|---|---|---|---|
| kipoi/kipoiseq | Python | Yes | Standard set of data-loaders for training and making predictions for DNA sequence-based models |
| kipoi/models | Python | Yes | Model zoo for genomics |
| Hugging Face | Python | Yes | Transformers library built for natural language processing applications and its platform that allows users to share machine learning models and datasets |
| SKOPS | Python | Yes | a Python library helping you share your scikit-learn based models and put them in production. At the moment, it includes tools to easily integrate models on the Hugging Face Hub |
| EUGENe | Python | Yes | computational framework for machine learning based modeling of regulatory sequences |
| Janggu | Python | Yes | Janggu is a python package that facilitates deep learning in the context of genomics |
| BioSimulators | Python, SBML | Yes | central registry of simulation engines and services for recommending specific tools. see also Benchmark-Models-PEtab |
| NCI Genetic Simulation Resources (GSR) | Python, R, C++ | Yes | Database of genetic simulation software tools |
| Name | Language | Active? | Description |
|---|---|---|---|
| GLUE (Graph-Linked Unified Embedding) | Python | Yes | Graph-linked unified embedding for single-cell multi-omics data integration |
| MOFA | R, Python | Yes | Multi-omic factor analysis |
| OmicsEV | R | Yes | OmicsEV: A tool for large scale omics data tables evaluation |
| SCENIC | R, Python | Yes | SCENIC Suite is a set of tools to study and decipher gene regulation. Its core is based on SCENIC (Single-Cell rEgulatory Network Inference and Clustering) which enables you to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data (using SCENIC) or the combination of single-cell RNA-seq and single-cell ATAC-seq data (using SCENIC+). |
| The Network Zoo | R, Python, MATLAB, C | Yes | a network biology package for the inference and analysis of gene regulatory networks |
| Name | Language | Active? | Description |
|---|---|---|---|
| pypath / OmniPath | Python, R | Yes | A Python module for molecular signaling prior knowledge processing |
| pyensembl | Python | Yes | annotation |
| eDGAR | Python | Yes | a database of Disease-Gene Associations |
| NDEx-The Network Data Exchange | Web, API | Yes | The NDEx Project provides an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. |
| Name | Language | Active? | Description |
|---|---|---|---|
| PyBDA | Python | Yes | A Python package for the analysis of biological data |
| PyBEL | Python | Yes | A Python module for biological expression language |
| pycellbase | Python | Yes | mainly microbial genomics |
| pygenometracks | Python | Yes | |
| skorch | Python | Yes | A scikit-learn compatible neural network library that wraps PyTorch. |
| TorchData | Python | Yes | A PyTorch repo for data loading and utilities |
see :ref:`roadmap`