Glossary
Cell
Graph components are qualified as cells after pixelator has carried out cell calling. However, further data analysis filtering can be done as demonstrated in our tutorials.
Component
Each graph is a representation of a putative cell but in the graph stage of the pipeline, we use the concept of a component to refer to them as pixelator hasn't yet qualified them as cells.
DNA pixels
DNA pixels and their use to map proteins in cell surfaces are a core innovation of Pixelgen Technologies. These are concatemers of DNA with predefined parts that allow MPX to be performed. For a brief introduction to MPX, check this document.
Edge
Edges are representations of molecules in the graphs generated by pixelator. Each edge connects together a combination of UPIA and UPIB and is decoded from an antibody barcode.
Graph Layout
Graphs are composed of nodes and edges linking them and most often, they represent abstract entities and relationships. In order to visualize graphs, a meaningful and readable representation of the graph is required. For some applications, the node location and distances are already know whereas for others, is not known or would produce an unreadable representation.
There are many layout strategies and in our visualization tutorial we explore some of those.
Modularity
The concept of modularity in networks is used to refer to the strength of the division in modules of the graph and how that metric is maximized when splitting in components after multiplet recovery.
MPX
Molecular Pixelation (MPX) is the name of the technology powering Pixelgen Technologies assays.
Nextflow
Nextflow is a workflow orchestration engine with a domain specific language (DSL) syntax that enables scalable and reproducible scientific workflows using software containers. It is compatible with the most common scripting languages and configurable to deploy complex parallel and reactive workflows on clouds and clusters.
nf-core
A community effort to collect a curated set of analysis pipelines using Nextflow with an open source philosophy. Nf-core pipeline adhere to strict guidelines with versioning, allowing easy reproducibility and validated releases, perfect for academic facilities. Workflow developers can use companion templates and tools help to validate pipeline code and simplify common tasks.
nf-core/pixelator
nf-core/pixelator is the name of Pixelgen Technologies nf-core open source workflow that is highly reliable, validated in different platforms and developed with reproducibility in mind.
Pixelator
Pixelator (with large P) is Pixelgen Technologies software suite to analyze MPX data. When we refer to Pixelator (in bold), i.e. in scientific publications or press releases, we mean any kind of software released by Pixelgen Technologies for the processing and analysis of MPX assays and derived data.
pixelator
Our software pixelator (with small p) is the library with the underlying logic for processing and analyzing MPX data, from raw FASTQ reads to pxl files. Pixelgen Technologies packages this library in software containers in order to use it as companion of nf-core/pixelator and thus, create highly reproducible workflows. By referring to pixelator (in bold), we mean the use of this library from the command-line, containerized images or as a programming library.
UMI
UMIs (Unique Molecular Identifiers) are tags made of unique nucleotide combinations attached to a molecule in order to provide with means to uniquely identify that particular molecule before amplification (e.g. PCR) and thus reduce quantitation biases Kivioja et al., 2011.
MPX uses UMIs in order to uniquely count antibody molecules, attached to each Ab-barcode there’s such a unique 8bp sequence.
With only 8 nucleotides, there is a limited amount of combinations (approx. 65k) to identify all molecules on a cell, therefore, we use the UMI+UPIA combination in order to enlarge this space (28 bp can tag more than 10^17 molecules).
UPI
UPI are a random nucleotide sequence (currently, 20bp in pixel design D21) that each DNA pixel concatemer has multiple copies of. Each pixel has its own UPI and given the randomness of this sequence and its length, it is highly unlike that two pixels have the same combination in the A or B sets.
UPIA
The random UPI of DNA pixel A.
UPIB
The random UPI of DNA pixel B.