ライフサイエンスコーパス: command line

1 all utilities in PhyloNet are invoked on the command line.

2 iles with a single line of user input at the command line.

3 cs of mass spectrometry data analysis at the command line.

4 via minimal efforts, such as using only one command line.

5 tire analysis can be performed with a single command line.

6 GLANET can be run using its GUI or on command line.

7 an be used through a web interface or in the command-line.

8 Users should be proficient at the command line; advanced users who wish to analyze larger

9 ch as EST cluster databases and conventional command-line analysis applications are integrated and ac

10 The pipeline is available as both a command line and a Galaxy graphical user interface tool.

11 lantSeg is free and open-source, with both a command line and a user-friendly graphical interface.

12 o computing resources, familiarity with Unix command line and basic experience with Python or R.

13 nt modifications made through the GUI or the command line and displays them in an interactive grid.

14 ally examining local genomic features on the command line and enables genome viewers to support huge

15 e 2.0 PDE reads input files specified on the command line and generates pedigree drawings without use

16 instant access to a range of pre-configured command line and graphical software applications, includ

17 t leverage the underlying database, and both command line and graphical tools for common analyses.

18 A-Lister is a lightweight command line and graphical user interface tool written i

19 utational literacy, including platforms with command line and graphical user interfaces.

20 The tools can both be run from the Unix command line and installed into visual workflow builders

21 aimed at users with basic experience of the command line and R.

22 Here we describe ped_draw a command line and web tool as a simple and easy solution

23 The utility runs from the command-line and can be easily integrated into a pipelin

24 COMKAT is equipped with command-line and graphic user interfaces from which the

25 well as MATLAB runtime scripts, through both command-line and graphic user interfaces.

26 It is available as a command-line and graphical user interface.

27 s in molecular imaging research and has both command-line and graphical user interfaces.

28 Queries can also be run from the command-line and the database can be queried directly th

29 accuracy, we made SIMMER available as both a command-line and web tool, with flexible input and outpu

30 e individually via its web server or via the command line, and is completely integrated with the wide

31 SyntenyQC is a command line app developed using Python version 3.10 and

32 We also provide a command line application which exercises all features pr

33 system on which Perl can be run, either as a command line application, in single or batch mode, or as

34 n be run from the web as well as a dedicated command line application, which allows easy integration

35 eely available at ; MSPC is distributed as a command-line application and an R package available from

36 sent amPEPpy, an open-source, multi-threaded command-line application for predicting AMP sequences us

37 This command-line application integrates sequence homology, n

38 However, there are only few command-line applications suitable for automated usage o

39 using gamma-distributed rate categories, and command-line arguments that preclude the use of accessor

40 ate through console menus or specify complex command-line arguments.

41 e VCF files and organized these tools into a command-line based utility named VCF-kit.

42 , usable through Graphical User Interface or command line-based version, aiming to serve as a protoco

43 Standalone programs are provided for command-line-based needs.

44 It is built upon RNATOPS, a command line C++ software package for the same purpose,

45 forqs is implemented as a command-line C++ program.

46 sists of a relational database (Isabl DB), a command line client (Isabl CLI), a RESTful API (Isabl AP

47 The JABAWS command-line client allows integration of JABAWS service

48 was implemented in Python 3.7, and runs as a command-line code under Linux or Unix.

49 of just 2-3x slowdown with respect to their command line counterparts.

50 variant tools consists of two command-line driven programs vtools and vtools_report.

51 equired to process metabolomic data by using command-line driven software programs.

52 s obtained from sequence alignments, and the command-line driven toolset could be used as a foundatio

53 ces for RBM are predominantly text-based and command-line driven.

54 Unfortunately, Rosetta is largely a command-line-driven software package which restricts its

55 s protocol requires basic familiarity with a command line environment.

56 bioinformatics tools rely on programming and command-line environments, which are challenging and tim

57 A JAVA cross-platform command line executable of ARACNe, together with all sou

58 SENECA and is available as a GUI client and command-line executable.

59 ing the source codes, which will equip their command line executables with user-friendly interface an

60 The Linux command-line executables for blastn and makembindex, doc

61 In addition to command-line execution, we integrated HTSQualC into the

62 th TIGERi could use the software without any command line experience.

63 available software that can be run from the command line for high throughput applications which can

64 ser-friendly, internet-enabled, open-source, command-line genome annotation and submission package to

65 r, these algorithms are often distributed as command line implementations that require expertise and

66 ta is developed in C/C++ and can be used via command line in MS Windows environments.

67 Genome aims to be easily integrated with the command line, including batch processing of data, and th

68 ailable to perform these operations from the command line, including BCFTools, vembrane, slivar, and

69 Cooltools provides a paired command line interface (CLI) and Python application prog

70 is project is implemented in Java 7, and the command line interface (CLI) is designed to integrate in

71 ) for Python programming, it also provides a command line interface (CLI) that enables utilization of

72 ead by Pycellerator, which includes a Python command line interface (CLI), a Python application progr

73 The combination of an easy to use, flexible command line interface and an underlying modular Python

74 It is available both as a command line interface and as a Python package with an a

75 A command line interface and the complete, open WebLogo so

76 Otherwise, LDRS can be used as a command line interface application within IDPConformerGe

77 Both tools are available with a command line interface as well as a graphical user inter

78 It provides a command line interface for easy integration into a bioin

79 ne application features a simple and concise command line interface for easy integration into high-th

80 art database search engines and a convenient command line interface for high-performance data process

81 entist with no programming experience, (2) a command line interface for scripting for a scientist wit

82 A command line interface has been developed to complement

83 however, learning to efficiently leverage a command line interface is a significant barrier in learn

84 It uses a command line interface to automatically call other progr

85 imitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly

86 The SurreyFBA is based on a command line interface to the GLPK solver distributed as

87 available from LanceOtron.molbiol.ox.ac.uk, command line interface via python is pip installable fro

88 Toolbox includes a graphical user interface, command line interface, and options for speed and accura

89 ducts, but GDBB has only been available on a command line interface, which is difficult to use for th

90 eatures are available via both graphical and command line interface.

91 tools have a graphical user interface and a command line interface.

92 ten in the C++ language and operated via the command line interface.

93 Pairtools provides modular command-line interface (CLI) tools that can be flexibly

94 s consisting of a browser-based interface, a command-line interface (CLI), and server-side components

95 functionalities are still accessed through a command-line interface (CLI).

96 kostkalab/aenmd.git), and as a containerized command-line interface (github.com/kostkalab/aenmd_cli.g

97 Its simple command-line interface allows for easy integration into

98 ree convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programm

99 AVIMM is supplemented by a command-line interface and a web front-end to query the

100 cludes a browser-accessible virtual desktop, command-line interface and computational notebook compat

101 Full documentation is available within the command-line interface as well as on IDPConformerGenerat

102 Additionally, we present a command-line interface for converting LPhy-specified mod

103 In addition, the package provides a command-line interface for users with scripting and prog

104 A command-line interface is also provided.

105 The command-line interface of svist4get allows for easy inte

106 VAT can either be run through a command-line interface or as a web application.

107 While the command-line interface readily integrates into bioinform

108 integrated into other software and offers a command-line interface that allows users to easily perfo

109 ols, eight new services and the release of a command-line interface to access, query and analyze data

110 MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent

111 graphical interface is provided as well as a command-line interface, both of which support many user-

112 res can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the w

113 tainer, and is equipped with a user-friendly command-line interface, thereby promoting its adoption i

114 rieve annotation from these catalogs via the command-line interface.

115 illions of molecules at a time with a simple command-line interface.

116 h a web-based graphical user interface and a command-line interface.

117 of a colleague familiar with the computer's command-line interface.

118 s usually requires prior experience with the command-line interface.

119 ations that are not feasible using the prior command-line interface.

120 executable file and to run that file from a command-line interface.

121 analysis in an automated pipeline using the command-line interface.

122 well-documented python library with a simple command-line interface.

123 to only those people who are confident with command line interfaces because it lacks a Graphical Use

124 Yet many immunoinformatics tools have command line interfaces only and can be difficult to ins

125 vert between file formats or learn different command line interfaces.

126 ecutable with a graphical user interface and command-line interfaces at

127 tional resources, data storage capacity, and command-line interfaces that limited user-friendliness.

128 f kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorit

129 isparate parts of needed analysis, have only command-line interfaces, and are difficult to extend/lin

130 n Core standard, includes both Web-based and command-line interfaces, and is fully open-source softwa

131 utorial describing our protocol and required command lines is included.

132 most of them require basic bioinformatic or command-line knowledge, which can limit the accessibilit

133 phisticated analyses that are independent of command-line knowledge.

134 there is no software that provides extensive command line level support for KEGG access and utilizati

135 and visualization tool based on the popular command-line Lucy1.

136 ser-friendly wrapping of a number of popular command-line metagenomics classification programs (Krake

137 mputers in both graphical user interface and command line modes.

138 h processing capabilities, and added several command line modules, all of which we briefly describe h

139 ssible both as a fast web-based tool and via command line (no coding skills are required to run the t

140 QuagmiR can be run from the command line on local machines, as well as on high-perfo

141 PRIMEGENS can be run from the command line on Unix/Linux platforms as a stand-alone pa

142 Java and provided as an ImageJ plugin with a command line option to perform more high-throughput anal

143 In addition to a command-line option, COMETS includes user-friendly Pytho

144 mat and various output formats, and provides command line options for tuning almost every aspect of t

145 In contrast to most command-line or batch interactions with Rosetta, Foldit

146 The toolbox, available as command-line or with a graphical user interface, enables

147 TreeMos can be run from the command line, or within a web browser allowing the relat

148 sent Genofunc, a toolkit offering a range of command line orientated functions for processing of raw

149 ET is currently available as part of the ET command-line package, and will be available as a web-ser

150 e heuristic alignment accuracy by optimizing command-line parameters in Bowtie 2, BWA-maximal exact m

151 The software is a command line perl script freely available as open source

152 Genomic Integration Site Tracker (GeIST), a command-line pipeline designed to map the integration si

153 THESEUS is a command line program for performing maximum likelihood (

154 tegrated Genome Viewer or with a stand-alone command line program.

155 nia' web interface, but can also be run as a command line program.

156 StochHMM provides a command-line program and C++ library that can implement

157 Here we present SequelTools, a command-line program containing three tools: Quality Con

158 Tevor and RIfin iDEntifier) is an HMM-based, command-line program that automates the identification a

159 e, we present a fast, simple and automatable command-line program that extracts optimal recombination

160 SCWRL is a command-line program that typically runs in a few second

161 MASS is a command-line program to perform meta-analysis of sequenc

162 ChIPs is implemented as a standalone command-line program written in C++ and is available fro

163 It can be used as a command-line program, a web application, or a utility li

164 commonly-used features of the 3DNA suite of command-line programs readily accessible.

165 to (i) execute and manage otherwise complex command-line programs, (ii) launch multiple exploratory

166 essly integrates with TPP and other external command-line programs, supporting various functionalitie

167 Additionally, we developed a command line Python tool, mirtop, to create and manage t

168 GSPA is available for download as a command-line Python package at

169 Physcraper is a command-line Python program that automates the update of

170 TRFolder is a command-line Python toolkit for TR-specific structure pr

171 ely available as a Bioconda package and as a command line script.

172 orts over 200 genomes and we have released a command-line script for running larger jobs and handling

173 an RNA visualization metaphor: Colorstock, a command-line script using ANSI terminal color; SScolor,

174 significant expertise in these software and command line scripting experience on Unix platforms, bes

175 le computational platform, comprising both a command-line set of tools and a C++ API, for the analysi

176 study, we introduce STEMSIM, a user-friendly command-line simulator of short-term evolutionary mutati

177 using these tools requires some scripting or command-line skills and familiarity with complex dataset

178 e sequencing analysis and assumes only basic command-line skills.

179 heir data without the need for sophisticated command-line skills.

180 We introduce a command line software application LC-IMS-MS Feature Find

181 We implemented a command line software tool and a web interface called w4

182 neration, and support for running both R and command-line software on local computers and computer cl

183 Command-line software plays a critical role in biology r

184 Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by user

185 mingbird was able to address applications in command line specified in JSON format or workflow descri

186 ling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBo

187 DF5 and is supported by a Python library and command line suite to create, read, inspect and manipula

188 es the following features: robust standalone command line support, improved pK(a) estimation via the

189 Synima runs quickly on a command line to generate informative and publication qua

190 my database and is easily manipulated at the command-line to specify a BLAST candidate's query-covera

191 BGT is a compact format, a fast command line tool and a simple web application for effic

192 A command line tool and a web interface are available to t

193 Easy-Prime is available both as a command line tool and an interactive PE design server at

194 Genomer is written as a command line tool and is an effort to make the manual pr

195 It can be found as a Python library and command line tool at pip, and Conda.

196 sis, we implement CGES both as a stand-alone command line tool available for download in GitHub and a

197 The command line tool can be used as a simple one liner comm

198 MONET is a command line tool for Linux, based on Docker and Singula

199 lti-Omic Graph Diagnosis (MOGDx), a flexible command line tool for the integration of multi-omic data

200 MetaPathPredict can be used as a command line tool or as a Python module, and both option

201 ation is available on PyPi for download as a command line tool or Python package and the source code

202 We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendl

203 we present peaks2utr, an easy-to-use Python command line tool that uses the UTR enrichment of single

204 is implemented in Rust and is available as a command line tool which can be compiled using the Rust t

205 ication at and can be installed locally as a command line tool with Bioconda.

206 We present MS-Helios, an easy to use command line tool with multiple built-in data processing

207 Here, we present grenedalf, a command line tool written in C++ that implements common

208 We demonstrate the command line tool's simplified Application Programming I

209 rk is available at (a python package) and (a command line tool).

210 e, we present STRprofiler, a Python package, command line tool, and Shiny application providing metho

211 GEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-bas

212 nstall and effectively utilize US-align as a command line tool, as an online web server, and as a plu

213 The command line tool, implemented in C++, is easily execute

214 We have developed a new Python command line tool, which is compatible with the widely a

215 Reaction Decoder is a robust command line tool, which performs this task with high ac

216 Jenever is implemented as a python-based command line tool.

217 In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome

218 comb-p is a command-line tool and a python library that manipulates

219 line model) out of 52 MVIAs in the form of a command-line tool and a web application.

220 Megadepth is available both as a command-line tool and as an R/Bioconductor package provi

221 GenoVi works as an easy-to-use command-line tool and provides customizable options to a

222 In summary, through the command-line tool and the web server, these protocols pr

223 Tabix is implemented as a free command-line tool as well as a library in C, Java, Perl

224 fication (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition

225 an OBO Tool") is an open source library and command-line tool for automating ontology development ta

226 resent BISQUE, a web server and customizable command-line tool for converting molecular identifiers a

227 Here, we introduce GRIEVOUS, a command-line tool for cross-dataset variant homogenizati

228 Here we present svist4get, a command-line tool for customizable generation of publica

229 In particular, is an efficient and reliable command-line tool for downloading articles in bulk from

230 Here, we introduced hifieval, a new command-line tool for measuring over- and under-correcti

231 A web server and a command-line tool for PhenoSV are available at .

232 Here, we introduce SNIKT, a command-line tool for sequence-independent visual confir

233 cture of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA

234 ser-friendly, end-to-end web application and command-line tool for the design of PE experiments.

235 ph (SG) is an open-source Python library and command-line tool for the generation and analysis of mol

236 Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motif

237 SciDataFlow is a fast, concurrent command-line tool paired with a simple Data Manifest spe

238 We present Epock, an efficient command-line tool that calculates pocket volumes from MD

239 Here I introduce GToTree, a command-line tool that can take any combination of fasta

240 er Notebook inside Google Colaboratory and a command-line tool that makes it easy to use AF2 while ex

241 ilable both as a web application at and as a command-line tool through Bioconda and PyPI.

242 amplimap is a command-line tool to automate the processing and analysi

243 ating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STAR file format i

244 lly, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics,

245 ne is easy to use via its web server or as a command-line tool, and can also make accurate prediction

246 Available as an open-source command-line tool, GMWI2 represents a timely, pivotal re

247 The BioPAX Validator is a command-line tool, Java library and online web service f

248 escribe the development and application of a command-line tool, Keanu, for visualizing and exploring

249 ble only as a computationally intensive UNIX command-line tool, restricting its use.

250 icly available through a web interface and a command-line tool, supporting future structure-function

251 Most usage is through the command-line tool, which runs on macOS, Linux, and Windo

252 NU General Public License v3, available as a command-line tool.

253 ble through a REST API and/or a downloadable command-line tool.

254 and to make those operations available as a command-line tool.

255 ere, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence dat

256 available for BAM file support as well as a command-line toolkit.

257 Command line tools are available for performing integrat

258 ng language and includes a flexible suite of command line tools as well as bindings to Python.

259 utilize WebAssembly to execute the original command line tools client-side directly in the web brows

260 ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-

261 stem further allows users to integrate local command line tools residing on their own computers throu

262 Modelled after Unix/GNU/Linux command line tools, individual programs perform a single

263 criptomes with similar efficiency to that of command line tools.

264 with an intuitive interface and as a set of command line tools; this allows biologists and bioinform

265 Many of the BiopTools command-line tools act as filters, taking a PDB (or PDBM

266 In addition, a series of command-line tools are provided to perform common bioinf

267 reamline complex bioinformatic workflows and command-line tools for bulk data analysis.

268 ogether, EMIM and PREMIM provide easy-to-use command-line tools for the analysis of pedigree data, gi

269 esentation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor d

270 The application can be executed using either command-line tools or a user-friendly Graphical User Int

271 We present a training model for use of command-line tools when the learner has little to no pri

272 g protein structure, and BiopTools, a set of command-line tools which exploit BiopLib.

273 r interface (GUI) to streamline usage of the command-line tools, calculate data from structure librar

274 the capabilities of many R/Bioconductor and command-line tools, it makes efficient use of existing s

275 of medical images, overcoming limitations of command-line tools.

276 GLINT is a user-friendly command-line toolset for fast analysis of genome-wide DN

277 ository, and we also provide source code for command line usage under Linux and Mac OS X.

278 ment and requiring a moderate knowledge of R command-line usage.

279 erface to make these tools available without command line use.

280 and is written in Python as both a suite of command line utilities and a Python application programm

281 Scorpio provides a set of command line utilities for classifying, haplotyping, and

282 Meta-eqtl is a set of command line utilities written in R, with some computati

283 a queries and downloads, alignment programs, command-line utilities and more.

284 The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invok

285 describe VIVA (VIsualization of VAriants), a command line utility and Jupyter Notebook based tool for

286 SplicePlot is a simple command line utility that produces intuitive visualizati

287 HMMSeg is a command-line utility for the scale-specific segmentation

288 ld network generator (SNG) is an open-source command-line utility that computes the hierarchical netw

289 Tersect is a lightweight, high-performance command-line utility which interprets and applies flexib

290 M files by a graphical user interface, and a command line validator that accompanies the library.

291 to a stand-alone version, we also provide a command line version of CovReport that can be integrated

292 In addition to a command line version, the suite has been integrated into

293 A command-line version of the toolset is available for dow

294 le as a web-server or a platform-independent command-line version.

295 Windows, web and command-line versions were developed to better serve dif

296 KBase) and are publicly available via API or command-line web interface.

297 sent, most ChIP-seq analysis tools adopt the command line, which lacks user-friendly interfaces.

298 It can run on the command line, within the R console, on the cloud platfor

299 ration tool that can be easily used from the command line without any deep learning expertise or spec

300 orkflows can be applied to new data from the command line without further user interaction.