Pinned Repositories
act_base
local Docker image for act
aikiknow
Aikido app using Polymer Starter Kit 2
benchie
A tool for automating benchmarks of programming assignments.
pyspark_blsspeller
Discovery of regulatory elements in related genomes using Apache Spark
FlowSOM_Python
The complete FlowSOM package known from R, now available in Python!
harpy
Single-cell spatial proteomics analysis that makes you happy!
hydra_hpc_example
Hydra HPC example
polygloty
VIB_Hackathon_June_2024
Code repository for the VIB Hackathon June 2024 on spatial omics. More info: https://hackmd.io/@berombau/BJetSxw8T
biosegment
BioSegment is a software stack to enable segmentation of microscopy data using machine learning models.
berombau's Repositories
berombau/benchie
A tool for automating benchmarks of programming assignments.
berombau/pyspark_blsspeller
Discovery of regulatory elements in related genomes using Apache Spark
berombau/act_base
local Docker image for act
berombau/aikiknow
Aikido app using Polymer Starter Kit 2
berombau/amltk
A build-it-yourself AutoML Framework
berombau/bioconda-recipes
Conda recipes for the bioconda channel.
berombau/deep-learning-biology
This repository contains the notebooks for the exercise sessions of the VIB Deep Learning for Biology workshop
berombau/configs
Config files used to define parameters specific to compute environments at different Institutions
berombau/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
berombau/FlowSOM
FlowSOM algorithm in Python, using self-organizing maps and minimum spanning tree for visualization and interpretation of cytometry data
berombau/gatsby-starter-netlify-cms
berombau/hydra
Hydra is a framework for elegantly configuring complex applications
berombau/hyperfine
A command-line benchmarking tool
berombau/itk-vtk-viewer
2D / 3D web image, mesh, and point set viewer using itk-wasm and vtk.js
berombau/mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
berombau/nextflow
A DSL for data-driven computational pipelines
berombau/Nictiz-Snowstorm
Modified docker build package for building and deploying snowstorm and elasticsearch containers. Also contains examples of dockerized python ingest scripts for loading releases.
berombau/ome-zarr-py
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
berombau/one-click-hugo-cms
berombau/openapi
OpenAPI Specification (OAS) for the Vatstack API.
berombau/preact-netlify
berombau/r_dev_test
berombau/scientific-python-lectures
Tutorial material on the scientific Python ecosystem
berombau/SpaceHack2022-Xenium
Our team work on Xenium data for the SpaceHack 2022
berombau/spatialdata
Modular storage and efficient manipulation of spatial multimodal molecular data in Python
berombau/spatialdata-io
berombau/spatialdata-plot
Static plotting for spatialdata
berombau/spatialdata-sandbox
berombau/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
berombau/thesis_supplementary
Supplementary files to thesis.