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Underlying R script for the investigation of immune cells. Script contains basic data processing, as well as a DE and monocle analysis.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Single nuclei transcriptomics data as .csv files from the Allen Brain atlas data set of mus musculus (https://celltypes.brain-map.org/) have been utilized as an input for scSynO. The underlying analysis is part of the manuscript entitled "Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling". Data anaylsis and visalizations were mainly generated with the Seurat R package (https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html)
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Here is the detailed R script to generate the input needed by scSynO for synthetic cell generation and classification model training.
The code that can be embedded into any other Seurat data processing workflow is:
cell_expression_target_cluster <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = "target_cluster_number")]) cell_expression_all_other_clusters <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = ...
Creator: Markus Wolfien
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
The pathways focused on SARS-CoV infections curated in Reactome. These pathways are work-in-progress.
Creators: Marc Gillespie, Robin Haw, Peter D'Eustachio
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified
The role of the interaction between the SARS-CoV-2 Spike protein and the renin-angiotensin pathway, in particular human ACE2 in pulmonary blood pressure regulation
Creators: Enrico Glaab, Andreas Ruepp, Corinna Montrone, Gisela Fobo
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. The number of infections increases daily, without any approved antiviral therapy. The recently released viral nucleotide sequence enables the identification of therapeutic targets, e.g., by analyzing integrated human-virus metabolic models. Investigations of changed metabolic processes after virus infections and the effect of knock-outs on the host and the virus can reveal new potential targets. Results: ...
Creators: Alina Renz, Andreas Dräger
Submitter: Martin Golebiewski
Model type: Not specified
Model format: SBML
Environment: Not specified
This model was created to showcase all functions of the SBML extension RAM. The model can be unr in deFBA with the python software deFBA-Python. The software is freely available at at https://tinyurl.com/yy8xu4v7
Creator: Henning Lindhorst
Submitter: Henning Lindhorst
Model type: Stoichiometric model
Model format: SBML
Environment: Not specified
Pathway: Assembly of the Replication Transcription Complex and Transcription
Creators: Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified