Title: Dirichlet Process Weibull Mixture Model for Survival Data
Description: Use Dirichlet process Weibull mixture model and dependent Dirichlet process Weibull mixture model for survival data with and without competing risks. Dirichlet process Weibull mixture model is used for data without covariates and dependent Dirichlet process model is used for regression data. The package is designed to handle exact/right-censored/ interval-censored observations without competing risks and exact/right-censored observations for data with competing risks. Inside each cluster of Dirichlet process, we assume a multiplicative effect of covariates as in Cox model and Fine and Gray model. For wrapper of the DPdensity function from the R package DPpackage (already archived by CRAN) that uses the Low Information Omnibus prior, please check (<https://github.com/mjmartens/DPdensity-wrapper-with-LIO-prior>).
Author: Yushu Shi
Maintainer: Yushu Shi <shiyushu2006@gmail.com>
Diff between DPWeibull versions 1.7 dated 2020-09-15 and 1.8 dated 2021-12-12
DESCRIPTION | 8 MD5 | 20 - R/RcppExports.R | 4 R/compdpm.R | 4 R/continue.R | 684 ++++++++++++++++++++++++------------------------- R/dpm.R | 116 ++++---- R/pred.R | 16 + data/deterioration.rda |binary data/survmedian.rda |binary man/dpweib.Rd | 5 src/noreg.cpp | 18 - 11 files changed, 451 insertions(+), 424 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures with
quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 2.8.0 dated 2021-07-16 and 2.8.5 dated 2021-12-12
DESCRIPTION | 22 ++++++++----------- MD5 | 44 +++++++++++++++++++-------------------- NEWS.md | 8 +++++++ R/base.R | 13 ++++++----- R/base_generics.R | 2 - R/base_hurdle.R | 13 +++++++---- R/base_surv.R | 11 ++++++--- R/base_utility.R | 2 - R/base_zi.R | 13 +++++++---- R/data.R | 2 - README.md | 2 - build/vignette.rds |binary inst/doc/qgcomp-vignette.R | 20 ++++++++++++++--- inst/doc/qgcomp-vignette.Rmd | 30 +++++++++++++++++++++----- inst/doc/qgcomp-vignette.html | 47 ++++++++++++++++++++++++++++++++---------- man/metals.Rd | 2 - man/qgcomp.boot.Rd | 4 +-- man/qgcomp.cox.boot.Rd | 4 +-- man/qgcomp.hurdle.boot.Rd | 6 ++--- man/qgcomp.zi.boot.Rd | 6 ++--- tests/test_asis.R | 14 ++++++------ tests/test_bootchooser.R | 14 ++++++------ vignettes/qgcomp-vignette.Rmd | 30 +++++++++++++++++++++----- 23 files changed, 199 insertions(+), 110 deletions(-)
Title: Partially Separable Quasi-Newton
Description: Provides quasi-Newton methods to minimize partially separable
functions. The methods are largely described by
Nocedal and Wright (2006) <doi:10.1007/978-0-387-40065-5>.
Author: Benjamin Christoffersen [cre, aut]
(<https://orcid.org/0000-0002-7182-1346>)
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between psqn versions 0.2.1 dated 2021-05-04 and 0.3.0 dated 2021-12-12
DESCRIPTION | 14 MD5 | 62 NAMESPACE | 5 NEWS | 12 R/RcppExports.R | 359 ++ R/psqn-package.R | 1 build/vignette.rds |binary inst/doc/psqn.html | 3728 +++++++++++++++------------ inst/doc/quick-intro.html | 417 +-- inst/generic_example.cpp | 30 inst/include/intrapolate.h | 4 inst/include/lp.h | 300 +- inst/include/psqn-bfgs.h | 24 inst/include/psqn-misc.h | 10 inst/include/psqn.h | 1574 +++++++---- inst/include/richardson-extrapolation.h |only inst/mlogit-ex.cpp | 193 + man/psqn.Rd | 138 man/psqn_bfgs.Rd | 13 man/psqn_generic.Rd | 165 + man/psqn_hess.Rd |only src/Makevars | 4 src/RcppExports.cpp | 144 - src/r-api.cpp | 745 +++++ src/test-intrapolate.cpp | 4 src/test-lp.cpp | 81 src/test-richardson-extrapolation.cpp |only tests/testthat/psqn_generic-glm-res-mask.RDS |only tests/testthat/psqn_generic-hess-res.RDS |only tests/testthat/test-R-api.R | 4 tests/testthat/test-cpp-api-true-hess.RDS |only tests/testthat/test-cpp-api.R | 54 tests/testthat/test-poly-ex.R | 6 tests/testthat/test-psqn-bfgs.R | 4 tests/testthat/test-psqn-generic.R | 58 35 files changed, 5583 insertions(+), 2570 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between coneproj versions 1.15 dated 2021-05-29 and 1.16 dated 2021-12-12
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 26 ++++---- R/coneproj.R | 173 +++++++++++++++++++++++++++++++++---------------------- inst/CITATION | 40 ++++++------ man/conc.Rd | 101 ++++++++++++++++---------------- man/conv.Rd | 105 +++++++++++++++++---------------- man/decr.Rd | 7 +- man/decr.conc.Rd | 7 +- man/decr.conv.Rd | 123 ++++++++++++++++++++------------------- man/incr.Rd | 7 +- man/incr.conc.Rd | 7 +- man/incr.conv.Rd | 7 +- man/shapereg.Rd | 2 14 files changed, 341 insertions(+), 277 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file,
import/export data from/to files with any format,
print strings with rich formats and colors);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.8.0 dated 2021-11-28 and 0.8.2 dated 2021-12-12
DESCRIPTION | 18 - MD5 | 46 +- NAMESPACE | 27 + NEWS.md | 18 + R/bruceR.R | 84 +++-- R/bruceR_basic.R | 99 +----- R/bruceR_stats_01_basic.R | 45 +- R/bruceR_stats_03_manova.R | 126 +++++-- R/bruceR_stats_04_regress.R | 717 ++++++++++++++++---------------------------- R/bruceR_stats_05_advance.R | 19 - R/bruceR_stats_06_plot.R | 2 R/deprecated.R | 129 +++++++ README.md | 11 build/partial.rdb |binary inst/CITATION | 2 man/EMMEANS.Rd | 27 - man/Freq.Rd | 20 - man/GLM_summary.Rd | 23 - man/HLM_summary.Rd | 72 +--- man/MANOVA.Rd | 9 man/bruceR-package.Rd | 1 man/model_summary.Rd | 23 - man/print_table.Rd | 2 man/regress.Rd | 44 +- 24 files changed, 803 insertions(+), 761 deletions(-)
Title: Database Interface and MariaDB Driver
Description: Implements a DBI-compliant interface to MariaDB
(<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>)
databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RMariaDB versions 1.1.2 dated 2021-09-06 and 1.2.0 dated 2021-12-12
.aspell |only DESCRIPTION | 20 MD5 | 52 NAMESPACE | 2 NEWS.md | 33 R/MariaDBConnection.R | 1 R/connect.R | 14 R/query.R | 10 R/table.R | 205 + README.md | 2 configure | 15 man/RMariaDB-package.Rd | 6 man/dbConnect-MariaDBDriver-method.Rd | 6 man/mariadb-tables.Rd | 9 src/DbConnection.cpp | 2 src/DbConnection.h | 2 src/Makevars.in | 2 src/MariaBinding.cpp | 75 src/MariaBinding.h | 4 src/MariaResultImpl.h | 2 src/MariaResultPrep.cpp | 4 src/MariaResultPrep.h | 2 src/MariaResultSimple.cpp | 2 src/MariaResultSimple.h | 2 tests/testthat/helper-DBItest.R | 14 tests/testthat/test-dbWriteTable.R | 40 tests/testthat/test-queries.R | 4 tools/tz.sql | 3640 +++++++++++++++++----------------- 28 files changed, 2240 insertions(+), 1930 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 2.2-0 dated 2021-06-23 and 2.3-0 dated 2021-12-12
DESCRIPTION | 10 MD5 | 48 ++-- NAMESPACE | 1 NEWS | 433 +---------------------------------------- R/bugtable.R | 137 +++++++----- R/news.R | 46 +++- build/vignette.rds |binary inst/CITATION | 8 inst/doc/bugfixes.Rnw | 34 ++- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/spatstatKnetsize.txt |only inst/doc/spatstatguisize.txt |only inst/doc/spatstatlocalsize.txt |only inst/doc/updates.R | 77 +++++-- inst/doc/updates.Rnw | 217 +++++++++++++++----- inst/doc/updates.pdf |binary man/bugfixes.Rd | 22 +- man/latest.news.Rd | 20 + man/spatstat-package.Rd | 2 man/spatstat.family.Rd |only vignettes/bugfixes.Rnw | 34 ++- vignettes/updates.Rnw | 217 +++++++++++++++----- 27 files changed, 639 insertions(+), 669 deletions(-)
Title: Database Interface Class
Description: 'R6' class interface for handling database connections using 'DBI' package as backend.
The class allows handling of connections to e.g. PostgreSQL, MariaDB and SQLite.
The purpose is having an intuitive object allowing straightforward handling of databases.
Author: Nikolaus Pawlowski [aut, cre, cph]
Maintainer: Nikolaus Pawlowski <niko@fr33.net>
Diff between rocker versions 0.1.2 dated 2021-11-17 and 0.2.1 dated 2021-12-12
rocker-0.1.2/rocker/man/figures |only rocker-0.2.1/rocker/DESCRIPTION | 12 rocker-0.2.1/rocker/MD5 | 93 + rocker-0.2.1/rocker/NAMESPACE | 74 + rocker-0.2.1/rocker/NEWS.md | 16 rocker-0.2.1/rocker/R/S3.R |only rocker-0.2.1/rocker/R/function.R | 18 rocker-0.2.1/rocker/R/rocker.R | 443 +++++++ rocker-0.2.1/rocker/README.md | 1627 +++++++++++++++++------------ rocker-0.2.1/rocker/build |only rocker-0.2.1/rocker/inst |only rocker-0.2.1/rocker/man/appendTable.Rd |only rocker-0.2.1/rocker/man/begin.Rd |only rocker-0.2.1/rocker/man/canConnect.Rd |only rocker-0.2.1/rocker/man/clearResult.Rd |only rocker-0.2.1/rocker/man/columnInfo.Rd |only rocker-0.2.1/rocker/man/commit.Rd |only rocker-0.2.1/rocker/man/connect.Rd |only rocker-0.2.1/rocker/man/createTable.Rd |only rocker-0.2.1/rocker/man/disconnect.Rd |only rocker-0.2.1/rocker/man/execute.Rd |only rocker-0.2.1/rocker/man/existsTable.Rd |only rocker-0.2.1/rocker/man/fetch.Rd |only rocker-0.2.1/rocker/man/fragments |only rocker-0.2.1/rocker/man/getInfoCon.Rd |only rocker-0.2.1/rocker/man/getInfoDrv.Rd |only rocker-0.2.1/rocker/man/getInfoRes.Rd |only rocker-0.2.1/rocker/man/getQuery.Rd |only rocker-0.2.1/rocker/man/getRowCount.Rd |only rocker-0.2.1/rocker/man/getRowsAffected.Rd |only rocker-0.2.1/rocker/man/getStatement.Rd |only rocker-0.2.1/rocker/man/hasCompleted.Rd |only rocker-0.2.1/rocker/man/isValidCon.Rd |only rocker-0.2.1/rocker/man/isValidDrv.Rd |only rocker-0.2.1/rocker/man/isValidRes.Rd |only rocker-0.2.1/rocker/man/listFields.Rd |only rocker-0.2.1/rocker/man/listObjects.Rd |only rocker-0.2.1/rocker/man/listTables.Rd |only rocker-0.2.1/rocker/man/newDB.Rd | 6 rocker-0.2.1/rocker/man/readTable.Rd |only rocker-0.2.1/rocker/man/removeTable.Rd |only rocker-0.2.1/rocker/man/rocker.Rd | 982 +++++++++++++++++ rocker-0.2.1/rocker/man/rollback.Rd |only rocker-0.2.1/rocker/man/sendQuery.Rd |only rocker-0.2.1/rocker/man/sendStatement.Rd |only rocker-0.2.1/rocker/man/setupDriver.Rd |only rocker-0.2.1/rocker/man/setupMariaDB.Rd |only rocker-0.2.1/rocker/man/setupPostgreSQL.Rd |only rocker-0.2.1/rocker/man/setupSQLite.Rd |only rocker-0.2.1/rocker/man/unloadDriver.Rd |only rocker-0.2.1/rocker/man/writeTable.Rd |only rocker-0.2.1/rocker/vignettes |only 52 files changed, 2568 insertions(+), 703 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' family of packages
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 2.2-0 dated 2021-06-14 and 2.3-0 dated 2021-12-12
DESCRIPTION | 8 ++++---- MD5 | 28 +++++++++++++++------------- NAMESPACE | 2 ++ NEWS | 21 +++++++++++++++++++++ R/primefactors.R | 12 +++++++----- R/tapplysum.R | 9 ++++++--- R/utiloptim.R | 19 ++++++++++++++++++- R/utiltext.R | 22 +++++++++++++--------- R/xycircle.R | 8 ++++---- R/xypolygon.R | 6 +++--- inst/doc/packagesizes.txt | 1 + man/primefactors.Rd | 2 ++ man/which.min.fair.Rd |only tests/circleseg.R |only tests/numerical.R | 46 +++++++++++++++++++++++++++++++++++++++------- tests/segments.R | 4 ++++ 16 files changed, 139 insertions(+), 49 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Single Cell Analysis and Differential Expression
Description: 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.
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between pagoda2 versions 1.0.7 dated 2021-11-15 and 1.0.8 dated 2021-12-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- README.md | 2 +- inst/rookServerDocs/js/aspectsTableViewer.js | 17 +++++------------ 4 files changed, 12 insertions(+), 19 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.4.3 dated 2021-07-20 and 0.4.4 dated 2021-12-12
DESCRIPTION | 12 +++--- MD5 | 37 +++++++++++---------- NAMESPACE | 1 NEWS.md | 15 ++++++++ R/RcppCWB_package.R | 13 +++---- R/RcppExports.R | 4 ++ R/checks.R | 3 + R/cl.R | 21 ++++++++++-- R/cqp.R | 2 - R/cwb.R | 43 ++++++++++++++++-------- R/misc.R | 18 ++++++---- README.md | 30 ++++++++--------- man/RcppCWB-packge.Rd | 13 +++---- man/cl_delete_corpus.Rd | 11 ++++++ man/corpus_is_loaded.Rd |only man/cqp_query.Rd | 2 - man/cwb_utils.Rd | 27 ++++++++------- src/RcppExports.cpp | 13 +++++++ src/cqp.cpp | 63 +++++++++++++++++++++++++++--------- tests/testthat/test_cwb_encode.R |only tests/testthat/test_delete_corpus.R |only 21 files changed, 221 insertions(+), 107 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-27 2.0
2021-05-27 1.1
Title: Technical Trading Rules
Description: A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.
Author: Joshua Ulrich
Maintainer: Joshua Ulrich <josh.m.ulrich@gmail.com>
Diff between TTR versions 0.24.2 dated 2020-09-01 and 0.24.3 dated 2021-12-12
CHANGES | 2 - DESCRIPTION | 6 +-- MD5 | 36 ++++++++++-------- NAMESPACE | 1 R/MovingAverages.R | 8 +++- R/WebData.R | 5 ++ R/keltnerChannels.R |only R/percentRank.R | 31 +++++++++++++--- R/runFun.R | 11 ++--- inst/unitTests/output.trend.rda |binary inst/unitTests/runit.TTR.MovingAverages.R | 9 ++++ inst/unitTests/runit.TTR.Trend.R | 8 ++++ inst/unitTests/runit.TTR.Volatility.R | 21 ++++++----- inst/unitTests/runit.TTR.runFun.R | 19 ++++++++-- man/WebData.Rd | 5 ++ man/keltnerChannels.Rd |only man/runPercentRank.Rd | 26 ++++++++++--- src/aroon.c | 57 ++++++++++++++---------------- src/moving_averages.c | 4 +- src/percent_rank.c | 16 ++++---- 20 files changed, 174 insertions(+), 91 deletions(-)
Title: Core Utilities for Single-Cell RNA-Seq
Description: Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.
Author: Viktor Petukhov [aut],
Ramus Rydbirk [aut],
Peter Kharchenko [aut],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between sccore versions 1.0.0 dated 2021-10-07 and 1.0.1 dated 2021-12-12
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 1 + R/graphs.R | 12 ++++++++---- R/helpers.R | 15 +++++++-------- R/plots.R | 10 ++++++---- README.md | 2 +- man/embeddingColorsPlot.Rd | 2 +- man/embeddingGroupPlot.Rd | 2 +- man/embeddingPlot.Rd | 2 +- man/extendMatrix.Rd | 4 ++-- man/fac2palette.Rd | 2 +- man/heatFilter.Rd | 1 - man/plapply.Rd | 4 ++++ man/smoothSignalOnGraph.Rd | 1 - man/val2ggcol.Rd | 2 +- src/RcppExports.cpp | 5 +++++ 17 files changed, 59 insertions(+), 46 deletions(-)