Showing 23 of total 23 results (show query)
terrytangyuan
scaffolder:Scaffolding Interfaces to Packages in Other Programming Languages
Comprehensive set of tools for scaffolding R interfaces to modules, classes, functions, and documentations written in other programming languages, such as 'Python'.
Maintained by Yuan Tang. Last updated 2 years ago.
code-generationpythonreticulatescaffolding
74.9 match 27 stars 6.13 score 9 scripts
react-r
reactR:React Helpers
Make it easy to use 'React' in R with 'htmlwidget' scaffolds, helper dependency functions, an embedded 'Babel' 'transpiler', and examples.
Maintained by Kent Russell. Last updated 6 months ago.
htmlhtmlwidgetsjavascriptreactreactjsweb
7.9 match 414 stars 14.09 score 109 scripts 175 dependents
ramnathv
htmlwidgets:HTML Widgets for R
A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.
Maintained by Carson Sievert. Last updated 1 years ago.
3.8 match 791 stars 19.05 score 7.4k scripts 3.1k dependents
rstudio
renv:Project Environments
A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Maintained by Kevin Ushey. Last updated 2 days ago.
3.3 match 1.0k stars 18.55 score 1.5k scripts 113 dependents
johncoene
packer:An Opinionated Framework for Using 'JavaScript'
Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM', 'yarn', and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' and 'yarn' packages, include 'TypeScript', 'React', or 'Vue' in web applications, and much more.
Maintained by John Coene. Last updated 7 months ago.
6.3 match 148 stars 6.25 score 1 scripts 2 dependentsrstudio
reticulate:Interface to 'Python'
Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.
Maintained by Tomasz Kalinowski. Last updated 1 days ago.
1.8 match 1.7k stars 21.07 score 18k scripts 427 dependents
cbailiss
pivottabler:Create Pivot Tables
Create regular pivot tables with just a few lines of R. More complex pivot tables can also be created, e.g. pivot tables with irregular layouts, multiple calculations and/or derived calculations based on multiple data frames. Pivot tables are constructed using R only and can be written to a range of output formats (plain text, 'HTML', 'Latex' and 'Excel'), including with styling/formatting.
Maintained by Christopher Bailiss. Last updated 1 years ago.
calculationshtmlhtmlwidgetlatexpivot-tablesvisualization
3.8 match 122 stars 8.08 score 358 scripts 1 dependents
corybrunson
ordr:A Tidyverse Extension for Ordinations and Biplots
Ordination comprises several multivariate exploratory and explanatory techniques with theoretical foundations in geometric data analysis; see Podani (2000, ISBN:90-5782-067-6) for techniques and applications and Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0> for foundations. Greenacre (2010, ISBN:978-84-923846) shows how the most established of these, including principal components analysis, correspondence analysis, multidimensional scaling, factor analysis, and discriminant analysis, rely on eigen-decompositions or singular value decompositions of pre-processed numeric matrix data. These decompositions give rise to a set of shared coordinates along which the row and column elements can be measured. The overlay of their scatterplots on these axes, introduced by Gabriel (1971) <doi:10.1093/biomet/58.3.453>, is called a biplot. 'ordr' provides inspection, extraction, manipulation, and visualization tools for several popular ordination classes supported by a set of recovery methods. It is inspired by and designed to integrate into 'tidyverse' workflows provided by Wickham et al (2019) <doi:10.21105/joss.01686>.
Maintained by Jason Cory Brunson. Last updated 12 days ago.
biplotdata-visualizationdimension-reductiongeometric-data-analysisgrammar-of-graphicslog-ratio-analysismultivariate-analysismultivariate-statisticsordinationtidymodelstidyverse
4.0 match 24 stars 7.26 score 28 scriptscbailiss
basictabler:Construct Rich Tables for Output to 'HTML'/'Excel'
Easily create tables from data frames/matrices. Create/manipulate tables row-by-row, column-by-column or cell-by-cell. Use common formatting/styling to output rich tables as 'HTML', 'HTML widgets' or to 'Excel'.
Maintained by Christopher Bailiss. Last updated 4 years ago.
htmlhtmlwidgettablesvisualization
3.8 match 37 stars 7.09 score 94 scripts
bioc
InPAS:Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.
Maintained by Jianhong Ou. Last updated 2 months ago.
alternative polyadenylationdifferential polyadenylation site usagerna-seqgene regulationtranscription
5.2 match 4.30 score 1 scripts
devopifex
windy:'Tailwind' for 'Shiny'
'Tailwind' for 'Shiny'.
Maintained by John Coene. Last updated 2 years ago.
6.6 match 38 stars 3.28 score
jonthegeek
beekeeper:Rapidly Scaffold API Client Packages
Automatically generate R package skeletons from 'application programming interfaces (APIs)' that follow the 'OpenAPI Specification (OAS)'. The skeletons implement best practices to streamline package development.
Maintained by Jon Harmon. Last updated 6 months ago.
3.0 match 54 stars 5.43 score 2 scripts
cran
bexy:Visualize and Parse the Output of 'BeXY'
Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.
Maintained by Madleina Caduff. Last updated 7 months ago.
15.3 match 1.00 score
hrbrmstr
vegalite:Tools to Encode Visualizations with the 'Grammar of Graphics'-Like 'Vega-Lite' 'Spec'
The 'Vega-Lite' 'JavaScript' framework provides a higher-level grammar for visual analysis, akin to 'ggplot' or 'Tableau', that generates complete 'Vega' specifications. Functions exist which enable building a valid 'spec' from scratch or importing a previously created 'spec' file. Functions also exist to export 'spec' files and to generate code which will enable plots to be embedded in properly configured web pages. The default behavior is to generate an 'htmlwidget'.
Maintained by Bob Rudis. Last updated 7 years ago.
data-visualizationdatavisualizationvega-litevega-lite-specvisualizationwidget
1.8 match 158 stars 7.60 score 84 scriptsbioc
CellNOptR:Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.
Maintained by Attila Gabor. Last updated 5 months ago.
cellbasedassayscellbiologyproteomicspathwaysnetworktimecourseimmunooncology
1.7 match 6.72 score 98 scripts 6 dependents
cynkra
cynkrathis:Simplify Project Scaffolding and Common 'renv' Related Tasks
Opionionated {renv} helper package by cynkra GmbH.
Maintained by Patrick Schratz. Last updated 4 months ago.
2.9 match 5 stars 3.88 score 1 scriptscran
leprechaun:Create Simple 'Shiny' Applications as Packages
Code generator for robust dependency-free 'Shiny' applications in the form of packages. It includes numerous convenience functions to create modules, include utility functions to create common 'Bootstrap' elements, setup a project from the ground-up, and much more.
Maintained by John Coene. Last updated 3 years ago.
5.6 match 1.70 score
pakillo
template:Generic template for data analysis projects structured as R packages
This package works as a template for new research or data analysis projects, under the idea of having everything (data, R scripts, functions and manuscript/reports) contained in the same package (a 'research compendium') to facilitate collaboration and promote reproducibility.
Maintained by Francisco Rodriguez-Sanchez. Last updated 4 years ago.
project-templateresearch-compendiumworkflow
1.9 match 175 stars 4.70 score 57 scriptscran
LoopRig:Integration and Analysis of Chromatin Loop Data
Common coordinate-based workflows involving processed chromatin loop and genomic element data are considered and packaged into appropriate customizable functions. Includes methods for linking element sets via chromatin loops and creating consensus loop datasets.
Maintained by Hassaan Maan. Last updated 5 years ago.
2.8 match 2.70 score
mgautierinra
poolfstat:Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data
Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in TreeMix, BayPass and SelEstim format).
Maintained by Mathieu Gautier. Last updated 4 months ago.
1.7 match 3.67 score 118 scriptsbioc
BUSpaRse:kallisto | bustools R utilities
The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.
Maintained by Lambda Moses. Last updated 5 months ago.
singlecellrnaseqworkflowstepcpp
0.5 match 9 stars 7.35 score 165 scripts
nifu-no
saros.base:Base Tools for Semi-Automatic Reporting of Ordinary Surveys
Scaffold an entire web-based report using template chunks, based on a small chapter overview and a dataset. Highly adaptable with prefixes, suffixes, translations, etc. Also contains tools for password-protecting, e.g. for each organization's report on a website. Developed for the common case of a survey across multiple organizations/sites where each organization wants to obtain results for their organization compared with everyone else. See 'saros' (<https://CRAN.R-project.org/package=saros>) for tools used for authors in the drafted reports.
Maintained by Stephan Daus. Last updated 1 months ago.
0.5 match 1 stars 5.98 score 7 scripts