Projects in Awesome Lists by simonsfoundation
A curated list of projects in awesome lists by simonsfoundation .
https://github.com/simonsfoundation/jp_gene_viz
A collection of visualizations for genomics related information for use with Jupyter notebooks.
Last synced: 10 Apr 2025
https://github.com/simonsfoundation/nnqp
Efficient numba based implementation of a nonnegative quadratic programming solver
Last synced: 10 Apr 2025
https://github.com/simonsfoundation/inferelator_ng
Inferelator refactor and generalization.
Last synced: 16 Jun 2025
https://github.com/simonsfoundation/spectrum-drug-tracker
Python files and datasets underlying the Spectrum Drug Tracker.
autism data data-visualization python python3
Last synced: 27 Feb 2026
https://github.com/simonsfoundation/pipeline
validated, scalable, minimalist variant detection pipeline
Last synced: 16 Feb 2026
https://github.com/simonsfoundation/franke_wolfe
A Numpy/Scipy implementation of the Franke Wolfe constrained optimization methodology.
Last synced: 06 Feb 2026
https://github.com/simonsfoundation/scaip
Tools for Calcium Imaging Analysis
Last synced: 24 Jan 2026
https://github.com/simonsfoundation/jp_svg_canvas
A very simple SVG canvas proxy widget for Jupyter visualizations
Last synced: 20 Apr 2026
https://github.com/simonsfoundation/spatial_transcriptomics_viz
visualization aids for spatial transcriptomics
Last synced: 29 Apr 2026
https://github.com/simonsfoundation/th17_trn_networks
Data and notebooks for "Leveraging ATAC-seq data for transcriptional regulatory inference in Th17 Cells" by Miraldi et al.
Last synced: 06 Oct 2025
https://github.com/simonsfoundation/regulatory_network_examples
Some regulatory network examples. You may need passwords to decrypt some data files.
Last synced: 13 Apr 2026
https://github.com/simonsfoundation/yeast_regulatory_network
Regulatory network visualization and workflow tools specialized for analysis of yeast biology.
Last synced: 16 Jun 2025
https://github.com/simonsfoundation/simons_jupyterhub
A collection of configurations and related information for creating a Jupyterhub instance for Simons Foundation.
Last synced: 16 Apr 2026
https://github.com/simonsfoundation/bioinfo_pipelines_cwl
Bioinformatics pipelines using Common Workflow Language and Docker.
Last synced: 15 Mar 2026
https://github.com/simonsfoundation/remap2b38
Remap a bam file to a given reference, and call variants with a choice of GATK HaplotypeCaller, Freebayes, Platypus.
Last synced: 24 Jul 2025
https://github.com/simonsfoundation/tr1_batfko
Critical role of the transcription factors IRF1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation
Last synced: 20 Apr 2026
https://github.com/simonsfoundation/format_phenotype_db
some scripts to format SPARK phenotype database to be used in WES QC and WGS QC.
Last synced: 14 Mar 2026
https://github.com/simonsfoundation/serverless-awslambda-container
Sample repository with code to deploy a custom Ubuntu container to AWS Lambda using the Serverless Framework.
Last synced: 06 Apr 2026
https://github.com/simonsfoundation/ida_publications_dashboard
ida_publications_dashboard
Last synced: 03 Jul 2025