saveDEasJSON

Save differential expression results as JSON

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.

Evan Biederstedt

conos

Clustering on Network of Samples

Viktor Petukhov

Nikolas Barkas

Peter Kharchenko

Weiliang Qiu

saveDEasJSON function

<dl><dt>de.results</dt>
<dd>differential expression results (default=NULL)</dd>
<dt>saveprefix</dt>
<dd>prefix for the differential expression output (default=NULL)</dd>
<dt>gene.metadata</dt>
<dd>data.frame with gene metadata (default=NULL)</dd>
<dt>cluster.sep.chr</dt>
<dd>character string of length 1 specifying a delimiter to separate cluster and app names (default='&lt;!!&gt;')</dd></dl>

Arguments

Save differential expression results as JSON — saveDEasJSON

<dl>

<dt>de.results</dt>
<dd>differential expression results (default=NULL)</dd>


<dt>saveprefix</dt>
<dd>prefix for the differential expression output (default=NULL)</dd>


<dt>gene.metadata</dt>
<dd>data.frame with gene metadata (default=NULL)</dd>


<dt>cluster.sep.chr</dt>
<dd>character string of length 1 specifying a delimiter to separate cluster and app names (default='&lt;!!&gt;')</dd>

</dl>

saveDEasJSON: Save differential expression results as JSON

Description

Usage

Value

Arguments