A system that provides a streamlined way of generating
    publication ready plots for known Single-Cell transcriptomics data in
    a “publication ready” format. This is, the goal is to automatically
    generate plots with the highest quality possible, that can be used
    right away or with minimal modifications for a research article.

Functions to implement the stability controlled 
    quasi-experiment (SCQE) approach to study the effects of 
    newly adopted treatments that were not assigned at random. This package 
    contains tools to help users avoid making statistical assumptions that rely 
    on infeasible assumptions. Methods developed in Hazlett (2019) 
    <doi:10.1002/sim.8717>.

Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) <doi:10.1002/0471667196.ess2129.pub2>, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) <doi:10.1080/10618600.2012.681238>, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.

Tools for scraping information from webpages and other XML contents, using XPath or CSS selectors.

The 'scrapeR' package utilizes functions that fetch and extract text content from specified web pages. It handles HTTP errors and parses HTML efficiently. The package can handle hundreds of websites at a time using the scrapeR_in_batches() command.

A group of functions to scrape data from different websites, for 
    academic purposes.

Routines for a collection of screen-and-clean type
        variable selection procedures, including UPS and GS.

Optimal hard thresholding of singular values. The procedure adaptively estimates the best singular value threshold under unknown noise characteristics. The threshold chosen by 'ScreeNOT' is optimal (asymptotically, in the sense of minimum Frobenius error) under the the so-called "Spiked model" of a low-rank matrix observed in additive noise. In contrast to previous works, the noise is not assumed to be i.i.d. or white; it can have an essentially arbitrary and unknown correlation structure, across either rows, columns or both. 'ScreeNOT' is proposed to practitioners as a mathematically solid alternative to Cattell's ever-popular but vague Scree Plot heuristic from 1966. 
    If you use this package, please cite our paper: David L. Donoho, Matan Gavish and Elad Romanov (2023). "ScreeNOT: Exact MSE-optimal singular value thresholding in correlated noise." Annals of Statistics, 2023 (To appear). <arXiv:2009.12297>.