simulated_umis

This data serves to develop cellpypes and to illustrate its functionality.
I made it up entirely.

datasets

Annotate single-cell RNA sequencing data manually based on
marker gene thresholds.
Find cell type rules (gene+threshold) through exploration,
use the popular piping operator '%>%' to reconstruct complex
cell type hierarchies.
'cellpypes' models technical noise to find positive and negative cells for
a given expression threshold and returns cell type labels or pseudobulks.
Cite this package as Frauhammer (2022) <doi:10.5281/zenodo.6555728> and
visit <https://github.com/FelixTheStudent/cellpypes> for tutorials and newest
features.

Felix Frauhammer

cellpypes

Cell Type Pipes for Single-Cell RNA Sequencing Data

simulated_umis function

A list with 4 entries:<dl>
<dt>raw</dt>
<dd>Raw (unnormalized) UMI counts for a handful of genes, last row are totalUMI.</dd><dt>neighbors</dt>
<dd>Indices of each cell's 50 nearest neighbors.</dd><dt>embed</dt>
<dd>Simulated UMAP embedding.</dd><dt>celltype</dt>
<dd>Cell type label that I used to simulate the data.</dd>
</dl>

Format

Simulated scRNAseq data — simulated_umis

A list with 4 entries:<dl>
<dt>raw</dt>
<dd>Raw (unnormalized) UMI counts for a handful of genes, last row are totalUMI.</dd>

<dt>neighbors</dt>
<dd>Indices of each cell's 50 nearest neighbors.</dd>

<dt>embed</dt>
<dd>Simulated UMAP embedding.</dd>

<dt>celltype</dt>
<dd>Cell type label that I used to simulate the data.</dd>


</dl>

simulated_umis: Simulated scRNAseq data

Description

Usage

Arguments

Format