papply

Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.

internal

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.

Evan Biederstedt

pagoda2

Single Cell Analysis and Differential Expression

Nikolas Barkas

Viktor Petukhov

Peter Kharchenko

Simon Steiger

Rasmus Rydbirk

papply function

<dl><dt>...</dt>
<dd>Additional arguments passed to mclapply(), lapply(), or BiocParallel::bplapply()</dd>
<dt>n.cores</dt>
<dd>Number of cores to use (default=parallel::detectCores())</dd>
<dt>mc.preschedule</dt>
<dd>See ?parallel::mclapply (default=FALSE). If TRUE then the computation is first divided to (at most) as many jobs are there are cores and then the jobs are started, each job possibly covering more than one value. If FALSE, then one job is forked for each value of X. The former is better for short computations or large number of values in X, the latter is better for jobs that have high variance of completion time and not too many values of X compared to mc.cores.</dd></dl>

Arguments

Parallel, optionally verbose lapply. See ?parallel::mclapply for more info. — papply

<dl>

<dt>...</dt>
<dd>Additional arguments passed to mclapply(), lapply(), or BiocParallel::bplapply()</dd>


<dt>n.cores</dt>
<dd>Number of cores to use (default=parallel::detectCores())</dd>


<dt>mc.preschedule</dt>
<dd>See ?parallel::mclapply (default=FALSE). If TRUE then the computation is first divided to (at most) as many jobs are there are cores and then the jobs are started, each job possibly covering more than one value. If FALSE, then one job is forked for each value of X. The former is better for short computations or large number of values in X, the latter is better for jobs that have high variance of completion time and not too many values of X compared to mc.cores.</dd>

</dl>

papply: Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.

Description

Usage

Value

Arguments