GML format
GML (Graph Modeling Language) is a text file format for saving network data.
Graph modularity
After a graph is divided into clusters, its modularity will be higher if there are a high number of connections between nodes from the same cluster and very few between nodes from different clusters. Modularity is represented on a scale 0-1 where 1 represents a perfectly modular graph.
It is a hierarchical data format for storing large amounts of data. For example, expression values for each cell can be saved as vectors, which can be accessed using cell names. One can load data for a cell without needing to load data for the rest of the cells.
HDF5 group
A node in the HDF5 hierarchy under which a dataset, for example PCA components, or another node can be stored.
Highly variable genes
Mapping score
Mapping score is one of key metric used by Nabo describe cell mapping. This score is given to each reference cell and is directly proportional to the number of target cells mapping to a reference cell.
Non zero mean
Non zero mean of a gene is its mean expression value calculated by considering only the cells where is was detected
These are an interactive programming interface. When we use this term we mean Jupyter (aka IPython) notebooks. Read more about them here.
Reference cells
The cells from a population/sample that will be used as base/reference cells, over which other cells are projected.
SNN graph
Graph created by identiyfing shared nearest neigbours between pairs of cells.
Target cells
The cells which would be individually mapped/projected onto reference cells.