A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input.  First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.

A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.

Extends the functionality of the package 'Synth' as detailed in Abadie, Diamond, and Hainmueller (2011) <doi:10.18637/jss.v042.i13>. Includes generating and plotting placebos, post/pre-MSPE (Mean Squared Prediction Error) significance tests and plots, and calculating average treatment effects for multiple treated units.

A normalization method for single-cell UMI count data using a 
  variance stabilizing transformation. The transformation is based on a 
  negative binomial regression model with regularized parameters. As part of the
  same regression framework, this package also provides functions for
  batch correction, and data correction. See Hafemeister and Satija (2019)
  <doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
  for more details.

Code for describing and manipulating scuba diving profiles 
	(depth-time curves) and decompression models, 
        for calculating the predictions of decompression models,
	for calculating maximum no-decompression time and decompression tables,
	and for performing mixed gas calculations.