baryshnikova-lab / safepyView external linksLinks
Python implementation of Spatial Analysis of Functional Enrichment (SAFE)
☆45Aug 26, 2025Updated 5 months ago
Alternatives and similar repositories for safepy
Users that are interested in safepy are comparing it to the libraries listed below
Sorting:
- Biological Network Integration using Convolutions☆64Jan 17, 2024Updated 2 years ago
- ☆13May 14, 2019Updated 6 years ago
- Bam to Pandas DataFrame, quickly☆13May 10, 2025Updated 9 months ago
- ☆13Dec 29, 2021Updated 4 years ago
- ☆12May 4, 2022Updated 3 years ago
- fast bgen parser for python☆16Jan 7, 2026Updated last month
- Graph Neural Network model for survival analysis from multi-omics data☆14Mar 9, 2022Updated 3 years ago
- The multiplex network of human diseases☆15Jul 3, 2025Updated 7 months ago
- 🍊🔬 Orange add-on for gene expression of single cell data☆17Nov 28, 2025Updated 2 months ago
- Graph Transformers for Large Graphs☆22Apr 26, 2024Updated last year
- ☆16Feb 25, 2017Updated 8 years ago
- Dynamic models for single-cell RNA-seq time series.☆40Sep 24, 2018Updated 7 years ago
- surrogate quantitative interpretability for deepnets☆24Aug 11, 2025Updated 6 months ago
- Online web tool for t-SNE analysis and interactive exploration of algorithm parameters☆20Nov 13, 2018Updated 7 years ago
- Code for further development of the mutual nearest neighbours batch correction method, as implemented in the batchelor package.☆22Jan 6, 2020Updated 6 years ago
- ☆19May 27, 2025Updated 8 months ago
- A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input ge…☆20Jan 20, 2026Updated 3 weeks ago
- A Python FASTA file Parser and Writer.☆17Sep 3, 2022Updated 3 years ago
- ☆21Jun 17, 2024Updated last year
- Quarto template for Public Library of Science☆23Jan 28, 2026Updated 2 weeks ago
- Scripts to run and benchmark scRNA-seq cell cluster labeling methods☆48May 23, 2020Updated 5 years ago
- Material for lecture at the EMBL Single Cell Course 2016☆47Apr 7, 2016Updated 9 years ago
- ☆26Mar 26, 2024Updated last year
- Tools for working with BUS files☆102May 27, 2025Updated 8 months ago
- Contextual AI models for single-cell protein biology☆96Feb 14, 2025Updated last year
- Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)☆27Jul 19, 2022Updated 3 years ago
- Peak caller for CUT&TAG data☆30Aug 18, 2022Updated 3 years ago
- An R wrapper for too-many-cells, for clustering single cells and analyzing cell clade relationships with colorful visualizations.☆26Mar 3, 2020Updated 5 years ago
- Scattering GCN: overcoming oversmoothness in graph convolutional networks☆25Jun 6, 2022Updated 3 years ago
- Algorithms for single-cell analysis☆29Jul 19, 2021Updated 4 years ago
- A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data☆35Jan 6, 2025Updated last year
- Count kmers with a more efficient (faster) hash table☆23Jun 8, 2024Updated last year
- ☆71Apr 17, 2024Updated last year
- ☆28Jan 28, 2020Updated 6 years ago
- Addressing the problem of predicting crime occurrence based on historic records☆11Nov 27, 2019Updated 6 years ago
- Data and analysis scripts for our Embryo Timecourse paper.☆68Dec 16, 2019Updated 6 years ago
- ☆131Nov 17, 2023Updated 2 years ago
- ☆10Jan 27, 2022Updated 4 years ago
- This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biolo…☆33Dec 10, 2020Updated 5 years ago