Packaged: 2014-07-15 18:28:00 UTC; John R Stevens

Packaged: 2014-12-10 19:48:53 UTC; John R Stevens

Title: SigWin-detector implementation in R
Maintainer: Wim de Leeuw <w.c.deLeeuw@uva.nl>
Description: Implementation of the SigWin-detector for the detection of
regions of increased or decreased gene expression (RIDGEs and
anti-RIDGES) in transcriptome maps and the presentation in so
called RIDGEOGRAMs as described by Marcia A. Inda et al. [BMC

Description: Uses logistic regression to model the probability of
detection as a function of covariates.  This model is then used
with observational survey data to estimate population size,
while accounting for uncertain detection.  See Steinhorst and

Description: Uses logistic regression to model the probability of detection as a function of covariates.
This model is then used with observational survey data to estimate population size, while
accounting for uncertain detection.  See Steinhorst and Samuel (1989).

person("Fieberg", "John",       email = "jfieberg@umn.edu",               role = c("aut")),
person("Schwarz", "Carl James", email = "cschwarz.stat.sfu.ca@gmail.com", role = c("aut","cre")))
Imports: formula.tools, Matrix, msm, plyr, stats, survey, utils
Suggests: car, data.table, ggplot2, kableExtra, knitr, readxl,
Maintainer: Schwarz Carl James <cschwarz.stat.sfu.ca@gmail.com>

Imports: formula.tools, Matrix, msm, plyr, mvtnorm, stats, survey,
Suggests: car, data.table, GGally, ggplot2, kableExtra, knitr, readxl,
reshape2, rmarkdown, tidyr, tidyverse, R.rsp

Title: Analysis of Single-Cell Chromatin Data
person(given = 'Tim', family = 'Stuart', email = 'tstuart@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),
person(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-7693-8957')),
person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9448-8833'))
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.
Imports: BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges,
IRanges, Matrix, Rsamtools, S4Vectors, Seurat, data.table,
dplyr, future, future.apply, ggplot2, ggseqlogo, irlba,
pbapply, tidyr, zoo, patchwork, Biostrings, BSgenome, gggenes,
Collate: 'data.R' 'generics.R' 'dimension_reduction.R' 'motifs.R'
Suggests: testthat (>= 2.1.0), chromVAR, SummarizedExperiment,
Author: Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>),