baryshnikova-lab / safepy
Python implementation of Spatial Analysis of Functional Enrichment (SAFE)
☆40Updated 11 months ago
Alternatives and similar repositories for safepy:
Users that are interested in safepy are comparing it to the libraries listed below
- ☆31Updated 3 years ago
- mygene is an easy-to-use Python wrapper to access MyGene.Info services.☆86Updated 2 weeks ago
- What you need to process the Quarterly DepMap-Omics releases from Terra☆114Updated this week
- GeneWalk identifies relevant gene functions for a biological context using network representation learning☆129Updated 5 months ago
- Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for …☆41Updated 5 months ago
- R package to access DoRothEA's regulons☆142Updated 11 months ago
- immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.☆64Updated this week
- Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.☆61Updated 3 years ago
- Grouping of Lymphocyte Interactions by Paratope Hotspots☆90Updated 4 years ago
- A simple pythonic interface to biomart.☆55Updated 4 years ago
- ☆23Updated 8 years ago
- Functional Associations using Variational Autoencoders☆39Updated 2 months ago
- Batch balanced KNN☆152Updated last year
- Tools for working with BUS files☆93Updated 3 months ago
- Code and documentation for the curation of cellxgene datasets☆39Updated this week
- Porting DESeq2 into python via rpy2☆68Updated last year
- Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotat…☆137Updated 2 months ago
- Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit☆49Updated last year
- COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data…☆59Updated 6 months ago
- bioinformatics plotting and tools☆54Updated 7 months ago
- kallisto | bustools workflow for pre-processing single-cell RNA-seq data☆117Updated 2 years ago
- dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data☆112Updated last week
- Geometry-preserving random sampling☆78Updated 3 months ago
- Material for lecture at the EMBL Single Cell Course 2016☆47Updated 8 years ago
- Tutorials and code for ISMB 2019 short course on Recent Advances in Statistical Methods and Computational Algorithms for Single-Cell Omic…☆39Updated 5 years ago
- code to run sei and obtain sei and sequence class predictions☆96Updated 2 years ago
- A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.☆87Updated 5 years ago
- Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…☆57Updated 10 months ago
- Compute generation probabilities of CDR3 amino acid and nucleotide sequences☆49Updated 3 years ago
- Hierarchical HotNet is an algorithm for finding hierarchies of active subnetworks.☆36Updated 5 years ago