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2021-sysbiocourse-acsb

Teaching material for Sysbio course 2021

2022-sysbiocourse-acsb

Teaching material for 2022 SysBio Course

2023-sysbiocourse-acsb

2024_ebi_grn

Materials for the 2024 course at EMBL-EBI: "Modelling gene regulation from transcriptomics and chromatin accessibility single-cell data".

albert_perez_rna_lipid

Analasing an RNA-lipidomic dataset from Albert Perez-Marti. They treated cell lines with different lipids and inhibitors and measured RNA and lipids.

astromouse

Spatial space data from mouse

benchmarkgurobi

berndt_egners_mastrobuoni

bio2bel_omnipath

OmniPath bio2bel plugin

bioconda-recipes

Conda recipes for the bioconda channel.

bioservices

a Python package that provides access to many Bioinformatices Web Services

birewire

An R package implementing high-performing routines for the randomisation of bipartite graphs preserving their node degrees.

bmp8b

A general purpose Python module for processing Full Moon Biotech PEX100 phosphoassay data and many other scripts for its further analysis in Pellegrinelli et al 2018

bradiplus

BraDiPluS (Braille Display Plugs Data Analysis) is an R package to process and analyse data produced using the microfluidic platform for functional drug screening of patient biopsies developed in collaboration with Merten group (EMBL).

breastcancercytof

modelling breast cancer cytof data with logic ODEs

cache-manager

A Python cache manager

carnival

CAusal Reasoning for Network Identification with integer VALue programming in R

carnival-bioconductor-dev

Provisional repository for the development of CARNIVAL package for Bioconductor

carnival_cropseq

causaltoxnet

supporting material for "Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury"

ccc_protocols

LIANA x Tensor-cell2cell Protocols

ccc_valencia_2023

Slides and materials for CCC workshop Valencia 2023

ccle_footprints

cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellnopt

Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.

cellnopt-feeder

Combining CNORFeeder with Dynamic-Feeder

cellnoptr

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

cellnoptr-maboss

CellNOptR with MaBoSS simulation