Showing 50 of total 50 results (show query)
trevorld
optparse:Command Line Option Parser
A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
Maintained by Trevor L. Davis. Last updated 10 months ago.
27.7 match 150 stars 12.86 score 13k scripts 32 dependents
jokergoo
GetoptLong:Parsing Command-Line Arguments and Simple Variable Interpolation
This is a command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptations for easier use in R. It also provides a simple way for variable interpolation in R.
Maintained by Zuguang Gu. Last updated 2 years ago.
23.3 match 17 stars 10.98 score 478 scripts 155 dependents
decisionpatterns
optigrab:Command-Line Parsing for an R World
Parse options from the command-line using a simple, clean syntax. It requires little or no specification and supports short and long options, GNU-, Java- or Microsoft- style syntaxes, verb commands and more.
Maintained by Christopher Brown. Last updated 6 years ago.
40.7 match 8 stars 5.80 score 39 scripts
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 1 months ago.
brainmrimrsmrshubspectroscopyfortran
25.2 match 25 stars 8.52 score 81 scripts
bioc
systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation
systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.
Maintained by Thomas Girke. Last updated 5 months ago.
geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
15.7 match 53 stars 11.56 score 344 scripts 3 dependents
ropensci
beastier:Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
Maintained by Richèl J.C. Bilderbeek. Last updated 24 days ago.
bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
21.3 match 11 stars 7.87 score 47 scripts 4 dependents
docopt
docopt:Command-Line Interface Specification Language
Define a command-line interface by just giving it a description in the specific format.
Maintained by Edwin de Jonge. Last updated 4 years ago.
14.2 match 213 stars 11.29 score 1.5k scripts 19 dependents
mlopez-ibanez
irace:Iterated Racing for Automatic Algorithm Configuration
Iterated race is an extension of the Iterated F-race method for the automatic configuration of optimization algorithms, that is, (offline) tuning their parameters by finding the most appropriate settings given a set of instances of an optimization problem. M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle, and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Maintained by Manuel López-Ibáñez. Last updated 1 months ago.
algorithm-configurationhyperparameter-tuningiraceoptimization-algorithms
14.4 match 63 stars 10.28 score 103 scripts 1 dependents
eddelbuettel
littler:R at the Command-Line via 'r'
A scripting and command-line front-end is provided by 'r' (aka 'littler') as a lightweight binary wrapper around the GNU R language and environment for statistical computing and graphics. While R can be used in batch mode, the r binary adds full support for both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path expression as the first line in scripts) as well as command-line use in standard Unix pipelines. In other words, r provides the R language without the environment.
Maintained by Dirk Eddelbuettel. Last updated 1 months ago.
13.6 match 314 stars 9.49 score 17 scripts
jonclayden
arrg:Flexible Argument Parsing for R Scripts
Argument parsing for R scripts, with support for long and short Unix-style options including option clustering, positional arguments including those of variable length, and multiple usage patterns which may take different subsets of options.
Maintained by Jon Clayden. Last updated 4 months ago.
command-linecommand-line-parser
28.3 match 7 stars 4.24 score 3 scripts
henrikbengtsson
R.utils:Various Programming Utilities
Utility functions useful when programming and developing R packages.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
7.0 match 63 stars 13.74 score 5.7k scripts 814 dependents
paulnorthrop
accessr:Command Line Tools to Produce Accessible Documents using 'R Markdown'
Provides functions to produce accessible 'HTML' slides, 'HTML', 'Word' and 'PDF' documents from input 'R markdown' files. Accessible 'PDF' files are produced only on a 'Windows' Operating System. One aspect of accessibility is providing a headings structure that is recognised by a screen reader, providing a navigational tool for a blind or partially-sighted person. A key aim is to produce documents of different formats easily from each of a collection of 'R markdown' source files. Input 'R markdown' files are rendered using the render() function from the 'rmarkdown' package <https://cran.r-project.org/package=rmarkdown>. A 'zip' file containing multiple output files can be produced from one function call. A user-supplied template 'Word' document can be used to determine the formatting of an output 'Word' document. Accessible 'PDF' files are produced from 'Word' documents using 'OfficeToPDF' <https://github.com/cognidox/OfficeToPDF>. A convenience function, install_otp() is provided to install this software. The option to print 'HTML' output to (non-accessible) 'PDF' files is also available.
Maintained by Paul J. Northrop. Last updated 2 days ago.
accessibilitycommand-linedigital-accessibilityrmarkdownrmarkdown-documentrmarkdown-slide
23.9 match 3.70 score 1 scripts
r-spatial
link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools
Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
Maintained by Chris Reudenbach. Last updated 4 months ago.
8.4 match 26 stars 9.05 score 78 scripts 1 dependentsbioc
psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.
Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.
sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-toolscpp
8.0 match 36 stars 6.95 score 31 scripts
ddalthorp
GenEst:Generalized Mortality Estimator
Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Maintained by Daniel Dalthorp. Last updated 2 years ago.
7.0 match 7 stars 7.81 score 55 scripts 2 dependentsr-spatial
qgisprocess:Use 'QGIS' Processing Algorithms
Provides seamless access to the 'QGIS' (<https://qgis.org>) processing toolbox using the standalone 'qgis_process' command-line utility. Both native and third-party (plugin) processing providers are supported. Beside referring data sources from file, also common objects from 'sf', 'terra' and 'stars' are supported. The native processing algorithms are documented by QGIS.org (2024) <https://docs.qgis.org/latest/en/docs/user_manual/processing_algs/>.
Maintained by Floris Vanderhaeghe. Last updated 5 months ago.
4.7 match 210 stars 10.09 score 175 scripts
djhshih
argparser:Command-Line Argument Parser
Cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.
Maintained by David J. H. Shih. Last updated 12 months ago.
7.3 match 5.88 score 1.6k scripts 1 dependents
yexiaoqingruc
carat:Covariate-Adaptive Randomization for Clinical Trials
Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria. See Ma W, Ye X, Tu F, and Hu F (2023) <doi: 10.18637/jss.v107.i02> for details.
Maintained by Xiaoqing Ye. Last updated 2 years ago.
20.8 match 2.02 score 35 scripts
s-fleck
colt:Command-Line Color Themes
A collection of command-line color styles based on the 'crayon' package. 'Colt' styles are defined in themes that can easily be switched, to ensure command line output looks nice on dark as well as light consoles.
Maintained by Stefan Fleck. Last updated 6 years ago.
7.9 match 10 stars 4.48 score 2 scripts 1 dependents
luciorq
condathis:Run Any CLI Tool on a 'Conda' Environment
Simplifies the execution of command line interface (CLI) tools within isolated and reproducible environments. It enables users to effortlessly manage 'Conda' environments, execute command line tools, handle dependencies, and ensure reproducibility in their data analysis workflows.
Maintained by Lucio Queiroz. Last updated 7 days ago.
bioinformaticscondareproducibilityreproducible-research
7.0 match 10 stars 5.00 score 1 scripts
bodkan
admixr:An Interface for Running 'ADMIXTOOLS' Analyses
An interface for performing all stages of 'ADMIXTOOLS' analyses (<https://reich.hms.harvard.edu/software>) entirely from R. Wrapper functions (D, f4, f3, etc.) completely automate the generation of intermediate configuration files, run 'ADMIXTOOLS' programs on the command-line, and parse output files to extract values of interest. This allows users to focus on the analysis itself instead of worrying about low-level technical details. A set of complementary functions for processing and filtering of data in the 'EIGENSTRAT' format is also provided.
Maintained by Martin Petr. Last updated 28 days ago.
bioinformaticspopgenpopulation-genetics
3.4 match 29 stars 7.42 score 91 scriptsbioc
RedeR:Interactive visualization and manipulation of nested networks
RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.
Maintained by Mauro Castro. Last updated 5 months ago.
guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology
3.7 match 6.65 score 107 scripts 7 dependents
mateiz
mlflow:Interface to 'MLflow'
R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Maintained by Matei Zaharia. Last updated 3 days ago.
3.8 match 1 stars 6.25 score 644 scripts
bioc
compcodeR:RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.
Maintained by Charlotte Soneson. Last updated 3 months ago.
immunooncologyrnaseqdifferentialexpression
2.5 match 11 stars 8.06 score 26 scripts
alexrecuenco
TexExamRandomizer:Personalizes and Randomizes Exams Written in 'LaTeX'
Randomizing exams with 'LaTeX'. If you can compile your main document with 'LaTeX', the program should be able to compile the randomized versions without much extra effort when creating the document.
Maintained by Alejandro Gonzalez Recuenco. Last updated 1 years ago.
4.0 match 1 stars 4.52 score 22 scripts
sahilseth
funr:Simple Utility Providing Terminal Access to all R Functions
A small utility which wraps Rscript and provides access to all R functions from the shell.
Maintained by Sahil Seth. Last updated 4 years ago.
3.4 match 34 stars 5.25 score 104 scriptsbioc
wpm:Well Plate Maker
The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the "plate effect" thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints.
Maintained by Helene Borges. Last updated 5 months ago.
guiproteomicsmassspectrometrybatcheffectexperimentaldesign
3.5 match 6 stars 4.78 score 7 scriptsbioc
spatialHeatmap:spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.
Maintained by Jianhai Zhang. Last updated 4 months ago.
spatialvisualizationmicroarraysequencinggeneexpressiondatarepresentationnetworkclusteringgraphandnetworkcellbasedassaysatacseqdnaseqtissuemicroarraysinglecellcellbiologygenetarget
2.7 match 5 stars 6.26 score 12 scripts
cran
batch:Batching Routines in Parallel and Passing Command-Line Arguments to R
Functions to allow you to easily pass command-line arguments into R, and functions to aid in submitting your R code in parallel on a cluster and joining the results afterward (e.g. multiple parameter values for simulations running in parallel, splitting up a permutation test in parallel, etc.). See `parseCommandArgs(...)' for the main example of how to use this package.
Maintained by Thomas Hoffmann. Last updated 7 years ago.
10.4 match 1.60 score
tiledb-inc
tiledbcloud:TileDB Cloud Platform R Client Package
The TileDB Cloud Platform API Client Package offers access to the TileDB Cloud service.
Maintained by John Kerl. Last updated 8 months ago.
2.7 match 1 stars 5.22 score 92 scripts
nelprin
domino:R Console Bindings for the 'Domino Command-Line Client'
A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite. 'Domino' is a service that makes it easy to run your code on scalable hardware, with integrated version control and collaboration features designed for analytical workflows (see <http://www.dominodatalab.com> for more information).
Maintained by Nick Elprin. Last updated 7 years ago.
7.0 match 1.56 score 36 scripts
regisoc
kibior:A Simple Data Management and Sharing Tool
An interface to store, retrieve, search, join and share datasets, based on Elasticsearch (ES) API. As a decentralized, FAIR and collaborative search engine and database effort, it proposes a simple push/pull/search mechanism only based on ES, a tool which can be deployed on nearly any hardware. It is a high-level R-ES binding to ease data usage using 'elastic' package (S. Chamberlain (2020)) <https://docs.ropensci.org/elastic/>, extends joins from 'dplyr' package (H. Wickham et al. (2020)) <https://dplyr.tidyverse.org/> and integrates specific biological format importation with Bioconductor packages such as 'rtracklayer' (M. Lawrence and al. (2009) <doi:10.1093/bioinformatics/btp328>) <http://bioconductor.org/packages/rtracklayer>, 'Biostrings' (H. Pagès and al. (2020) <doi:10.18129/B9.bioc.Biostrings>) <http://bioconductor.org/packages/Biostrings>, and 'Rsamtools' (M. Morgan and al. (2020) <doi:10.18129/B9.bioc.Rsamtools>) <http://bioconductor.org/packages/Rsamtools>, but also a long list of more common ones with 'rio' (C-h. Chan and al. (2018)) <https://cran.r-project.org/package=rio>.
Maintained by Régis Ongaro-Carcy. Last updated 4 years ago.
dataimportdatarepresentationthirdpartyclientdata-sciencedatabasedatasetselasticsearchelasticsearch-clientpush-pullsearchsearch-engine
2.3 match 3 stars 4.48 score 8 scripts
rnabioco
valr:Genome Interval Arithmetic
Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data. Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.
Maintained by Kent Riemondy. Last updated 8 days ago.
bedtoolsgenomeinterval-arithmeticcpp
1.0 match 90 stars 9.69 score 227 scripts
piecepackr
ppn:Portable Piecepack Notation Parser
Parse "Portable Piecepack Notation" files. This allows you to visualize the moves for over one hundred board games.
Maintained by Trevor L. Davis. Last updated 3 days ago.
3.6 match 2.65 score 2 scripts 1 dependentsropensci
phylogram:Dendrograms for Evolutionary Analysis
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
Maintained by Shaun Wilkinson. Last updated 5 years ago.
1.0 match 11 stars 8.53 score 228 scripts 9 dependentsropensci
MODIStsp:Find, Download and Process MODIS Land Products Data
Allows automating the creation of time series of rasters derived from MODIS satellite land products data. It performs several typical preprocessing steps such as download, mosaicking, reprojecting and resizing data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional quality indicators should be extracted from aggregated MODIS quality assurance layers and, in the case of surface reflectance products, which spectral indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing users to automatically update time series related to a MODIS product whenever a new image is available. For additional documentation refer to the following article: Busetto and Ranghetti (2016) <doi:10.1016/j.cageo.2016.08.020>.
Maintained by Luigi Ranghetti. Last updated 8 months ago.
gdalmodismodis-datamodis-land-productspeer-reviewedpreprocessingremote-sensingsatellite-imagerytime-series
1.0 match 156 stars 8.04 score 86 scripts 1 dependents
lucarraro
traudem:Use TauDEM
Simple trustworthy utility functions to use TauDEM (Terrain Analysis Using Digital Elevation Models <https://hydrology.usu.edu/taudem/taudem5/>) command-line interface. This package provides a guide to installation of TauDEM and its dependencies GDAL (Geopatial Data Abstraction Library) and MPI (Message Passing Interface) for different operating systems. Moreover, it checks that TauDEM and its dependencies are correctly installed and included to the PATH, and it provides wrapper commands for calling TauDEM methods from R.
Maintained by Luca Carraro. Last updated 11 months ago.
1.3 match 12 stars 5.79 score 17 scripts
paleolimbot
exifr:EXIF Image Data in R
Reads EXIF data using ExifTool <https://exiftool.org> and returns results as a data frame. ExifTool is a platform-independent Perl library plus a command-line application for reading, writing and editing meta information in a wide variety of files. ExifTool supports many different metadata formats including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP and ID3, as well as the maker notes of many digital cameras by Canon, Casio, FLIR, FujiFilm, GE, HP, JVC/Victor, Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo, Sigma/Foveon and Sony.
Maintained by Dewey Dunnington. Last updated 4 years ago.
1.0 match 35 stars 6.24 score 150 scripts 2 dependentstrevorld
xmpdf:Edit 'XMP' Metadata and 'PDF' Bookmarks and Documentation Info
Edit 'XMP' metadata <https://en.wikipedia.org/wiki/Extensible_Metadata_Platform> in a variety of media file formats as well as edit bookmarks (aka outline aka table of contents) and documentation info entries in 'pdf' files. Can detect and use a variety of command-line tools to perform these operations such as 'exiftool' <https://exiftool.org/>, 'ghostscript' <https://www.ghostscript.com/>, and/or 'pdftk' <https://gitlab.com/pdftk-java/pdftk>.
Maintained by Trevor L Davis. Last updated 12 months ago.
1.0 match 5 stars 5.18 score 1 scripts 1 dependentsbioc
primirTSS:Prediction of pri-miRNA Transcription Start Site
A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.
Maintained by Pumin Li. Last updated 5 months ago.
immunooncologysequencingrnaseqgeneticspreprocessingtranscriptiongeneregulation
1.0 match 4.48 score 2 scriptsbioc
ddCt:The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
Maintained by Jitao David Zhang. Last updated 5 months ago.
geneexpressiondifferentialexpressionmicrotitreplateassayqpcr
1.0 match 4.38 score 8 scriptsbioc
HelloRanges:Introduce *Ranges to bedtools users
Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.
Maintained by Michael Lawrence. Last updated 5 months ago.
sequencingannotationcoveragegenomeannotationdataimportsequencematchingvariantannotation
1.0 match 4.19 score 26 scripts 1 dependents
stla
findInFiles:Find Pattern in Files
Creates a HTML widget which displays the results of searching for a pattern in files in a given folder. The results can be viewed in the 'RStudio' viewer pane, included in a 'R Markdown' document or in a 'Shiny' application. Also provides a 'Shiny' application allowing to run this widget and to navigate in the files found by the search. Instead of creating a HTML widget, it is also possible to get the results of the search in a 'tibble'. The search is performed by the 'grep' command-line utility.
Maintained by Stéphane Laurent. Last updated 11 months ago.
1.0 match 12 stars 3.86 score 12 scripts
richelbilderbeek
netmhc2pan:Interface to 'NetMHCIIpan'
The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at <https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/> or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.
1.0 match 1 stars 3.70 score 8 scriptseddelbuettel
RcppGetconf:'Rcpp' Interface for Querying System Configuration Variables
The 'getconf' command-line tool provided by 'libc' allows querying of a large number of system variables. This package provides similar functionality.
Maintained by Dirk Eddelbuettel. Last updated 2 months ago.
1.1 match 1 stars 3.54 score 2 scripts
mariushofert
crop:Graphics Cropping Tool
A device closing function which is able to crop graphics (e.g., PDF, PNG files) on Unix-like operating systems with the required underlying command-line tools installed.
Maintained by Marius Hofert. Last updated 1 years ago.
1.0 match 1.28 score 19 scriptscran
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.
1.0 match 1.00 score