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  • |{{#vardefine:app|c-wap}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/C-WAP}}
    2 KB (281 words) - 13:16, 15 August 2022
  • |{{#vardefine:app|netcdf-c}}
    2 KB (279 words) - 14:53, 3 June 2022
  • NCBI C++ Toolkit provides free, portable, public domain libraries with no restrict
    3 KB (306 words) - 17:47, 15 August 2022
  • File:2012-04-19-Parallel Processing-C Taylor.ppt
    (1.42 MB) - 16:10, 19 April 2012

Page text matches

  • ...n-us/intel-parallel-studio-xe Intel Compiler Suite] provides Fortran and C/C++ compilers and is preferred compiler option on hipergator. The [https://gcc.gnu.org GNU Compiler Suite] provides Fortran and C/C++ compilers.
    1 KB (159 words) - 22:30, 26 July 2021
  • mpicc ( C source) mpiCC (C++ source)
    3 KB (298 words) - 19:00, 15 August 2022
  • ...the 'glue code' required for the above target languages to call into the C/C++ code. SWIG can also export its parse tree in the form of XML and Lisp s-e
    3 KB (414 words) - 17:48, 15 August 2022
  • ...ng dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data. ..., Heard E., Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x
    3 KB (432 words) - 18:17, 15 August 2022
  • "Boost provides free peer-reviewed portable C++ source libraries. We emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and u
    3 KB (350 words) - 13:06, 15 August 2022
  • sander -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd mpiexec sander.MPI -O -i amber.in -o amber.log -p amber.prmtop -c amber.inpcrd
    1 KB (167 words) - 17:38, 26 June 2017
  • |{{#vardefine:url|http://xerces.apache.org/#xerces-c}} ...or parsing, generating, manipulating, and validating XML documents. Xerces-C++ is faithful to the XML 1.0 and 1.1 recommendations and many associated st
    3 KB (306 words) - 21:29, 6 December 2019
  • ...n rates from population genetic data. The package is available either as C/C++ source code.
    2 KB (296 words) - 17:09, 10 June 2022
  • The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc+
    2 KB (251 words) - 16:55, 15 August 2022
  • ...ython interface provides a high-level yet efficient API to use most of the C++ interface with ease.
    3 KB (325 words) - 14:13, 15 August 2022
  • ...stq raw data files and command line tools for feature annotation on the Hi-C maps.
    2 KB (273 words) - 19:12, 15 August 2022
  • FreeSASA is a C library and C++ command line tool for calculating Solvent Accessible Surface Area (SASA) Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:1
    2 KB (276 words) - 16:49, 15 August 2022
  • ...possible tree topology. To run ASAQ it is necessary to have installed the C++ linear algebra library Armadillo ...//arma.sourceforge.net/armadillo_joss_2016.pdf Armadillo: a template-based C++ library for linear algebra]. Journal of Open Source Software, Vol. 1, pp.
    3 KB (374 words) - 15:10, 1 June 2022
  • The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libs
    2 KB (298 words) - 20:44, 15 August 2022
  • annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba and
    3 KB (406 words) - 14:47, 15 August 2022
  • Intel® Cluster Studio features the acclaimed Intel Fortran and C++ Compilers. These performance-oriented compilers can deliver a remarkable Intel Compilers support OpenMP. Developers using C or C++ can create and manage portable, shared-memory parallelism in their applic
    3 KB (332 words) - 19:30, 10 June 2022
  • ...GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC® directives, and CUDA®. GPU-accelerated math libra
    3 KB (334 words) - 19:06, 6 June 2022
  • ...e, G. D., Hunagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S-H., Childs, K. L., Sun, Y., Jiang, N, Yandell, M. 20
    3 KB (329 words) - 21:22, 6 December 2019
  • ...ing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. See http://dlib.net for the main project do
    2 KB (269 words) - 13:11, 4 May 2020
  • A tool to scaffold long read assemblies with Hi-C Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact in
    2 KB (267 words) - 20:06, 10 June 2022
  • Armadillo is a high quality C++ linear algebra library, aiming towards a good balance between speed and e ...://arma.sourceforge.net/armadillo_nicta_2010.pdf Armadillo: An Open Source C++ Linear Algebra Library for Fast Prototyping and Computationally Intensive
    2 KB (269 words) - 14:33, 12 August 2022
  • ...marsh, P. N. Brown, K. E. Grant, S. L. Lee, R. Serban, D. E. Shumaker, and C. S. Woodward, "SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equa * R. Serban and A. C. Hindmarsh, "CVODES: the Sensitivity-Enabled ODE Solver in SUNDIALS," Proce
    3 KB (367 words) - 13:45, 13 June 2022
  • ...re (C), MagickWand (C), ChMagick (Ch), ImageMagickObject (COM+), Magick++ (C++), JMagick (Java), L-Magick (Lisp), Lua, NMagick (Neko/haXe), Magick.NET (
    3 KB (380 words) - 18:46, 15 August 2022
  • |{{#vardefine:app|c-wap}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/C-WAP}}
    2 KB (281 words) - 13:16, 15 August 2022
  • ...e that the Fortran module man not have all supporting binaries that netcdf-c module has.
    3 KB (383 words) - 14:53, 3 June 2022
  • ...ry for astrophysical simulations and models. Grackle has interfaces for C, C++, Fortran, and Python codes and provides:
    2 KB (294 words) - 17:18, 15 August 2022
  • BERTopic is a topic modeling technique that leverages transformers and c-TF-IDF to create dense clusters allowing for easily interpretable topics wh [https://zenodo.org/record/4719700 BERTopic: Leveraging BERT and c-TF-IDF to create easily interpretable topics.]
    2 KB (283 words) - 14:00, 27 May 2022
  • PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus
    2 KB (296 words) - 20:25, 12 August 2022
  • J. A. Anderson, C. D. Lorenz, and A. Travesset. General purpose molecular dynamics simulation ...D. Nguyen, J. A. Anderson, P. Liu, F. Spiga, J. A. Millan, D. C. Morse, S. C. Glotzer. Strong scaling of general-purpose molecular dynamics simulations
    5 KB (607 words) - 15:40, 6 June 2022
  • The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General
    2 KB (300 words) - 17:27, 15 August 2022
  • ...des several hundreds of computer vision algorithms. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with Op
    2 KB (283 words) - 21:31, 6 December 2019
  • ...M., Mirza, G., Butler, H., Clouston, P., Basset, A.S., Seller, A., Holmes, C., and Ragoussis, J. QuantiSNP: an Objective Bayes Hidden-Markov Model to de
    2 KB (297 words) - 20:29, 12 August 2022
  • ...te (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the ​OpenGIS Simple Features for SQL spatial predica
    3 KB (307 words) - 17:05, 15 August 2022
  • ...orage and worklist servers. DCMTK is is written in a mixture of ANSI C and C++. It comes in complete source code and is made available as "open source"
    3 KB (304 words) - 20:31, 10 June 2022
  • pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets o
    3 KB (303 words) - 20:08, 31 May 2022
  • ...olkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python. ...methods, basic blocks, and statements as well as event-based sampling. All C++ language features are supported including templates and namespaces. The A
    3 KB (443 words) - 17:37, 6 June 2022
  • Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "F Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, H
    3 KB (404 words) - 20:38, 12 August 2022
  • ...ary fully written from scratch in pure ANSI C. It is designed to offer for C programmers common data structures with powerful algorithms, and hidden imp
    3 KB (305 words) - 15:37, 6 June 2022
  • ...olkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. ...h instrumentation of functions, methods, basic blocks, and statements. All C++ language features are supported including templates and namespaces. The A
    4 KB (575 words) - 21:31, 6 December 2019
  • ...liquid, solid, or gaseous state. It is a open source software, written in C++ and developed at Sandia laboratory. It can be used to model atomic, polym ...CMAKE_INSTALL_PREFIX=<target_lammps_dir> -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake ../cmake
    3 KB (467 words) - 23:34, 20 August 2021
  • ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data ...embly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data. Nature Plants, doi:10.1038/s41477-019-0487-8 (2019).
    3 KB (299 words) - 12:35, 12 August 2022
  • * C * C++
    3 KB (322 words) - 19:19, 15 August 2022
  • ...n: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. ...A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science eaal3327. Published online ahea
    3 KB (328 words) - 17:51, 10 June 2022
  • Dohm JC, Lottaz C, Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read a Dohm JC, Lottaz C, Borodina T, Himmelbauer H Substantial biases in ultra-short read data sets
    3 KB (310 words) - 14:30, 3 June 2022
  • ...evelopers can launch compute kernels written using a limited subset of the C programming language on a GPU. ...wget -q https://raw.github.com/smistad/OpenCL-Getting-Started/master/main.c
    3 KB (363 words) - 20:47, 10 June 2022
  • ...rnals.org/content/early/2014/10/22/bioinformatics.btu704.short Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatic Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR. Fast and accurate genotype imputa
    3 KB (332 words) - 18:31, 10 June 2022
  • ...le, D. E.; Vega Thurber, R. L.; Knight, R.; Beiko, R. G.; and Huttenhower, C. Nature Biotechnology, 1-10. 8 2013.]
    3 KB (344 words) - 18:28, 10 June 2022
  • ...many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
    3 KB (330 words) - 18:19, 15 August 2022
  • .... Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
    3 KB (322 words) - 13:32, 13 June 2022
  • maqindex -i -c consensus.cns all.map; maqview -c consensus.cns all.map
    3 KB (377 words) - 19:47, 12 August 2022
  • BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks proven * A C++ library 'seqio' for efficient I/O of large NGS data files
    3 KB (362 words) - 12:54, 15 August 2022
  • [http://mbe.oxfordjournals.org/content/24/2/412.abstract?etoc C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimati ...l.pdf?ijkey=BIwQBlPEqeEiojQ&keytype=ref B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010). BUCKy: Gene tree / species tree reconciliation with the Bayes
    3 KB (386 words) - 13:15, 15 August 2022
  • ...Elastix, making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.
    3 KB (365 words) - 15:30, 3 June 2022
  • | C || icc || ''icc compiler_options example.c'' | C++ || icpc || ''icpc compiler_options -o example.exe example.cxx''
    5 KB (662 words) - 18:58, 15 August 2022
  • ===cuda_bm.c=== {{#fileAnchor: cuda_bm.c}}
    11 KB (1,462 words) - 20:33, 21 June 2017
  • Mamba is a reimplementation of the conda package manager in C++. core parts of mamba are implemented in C++ for maximum efficiency
    3 KB (429 words) - 20:16, 3 June 2022
  • ...orBoard 2.4.0 at '''<nowiki>http://localhost:6006/</nowiki>''' (Press CTRL-C to quit)
    1 KB (184 words) - 18:18, 20 January 2022
  • VBScript, VBA, JavaScript, .NET (C#/VB), Java, JSP, C++, PHP, Perl, Python,
    3 KB (397 words) - 13:26, 15 August 2022
  • Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST Author : Edgar, Robert C.
    4 KB (557 words) - 20:53, 12 August 2022
  • [1] H. Wang, J. W. Suh, S. Das, J. Pluta, C. Craige, P. Yushkevich, "Multi-atlas segmentation [2] H. Wang, S. R. Das, J. W. Suh, M. Altinay, J. Pluta, C. Craige, B. B. Avants, and P. A. Yushkevich,
    3 KB (390 words) - 20:22, 3 June 2022
  • "/drives/c/Program Files/Xpra/Xpra" "$@"
    2 KB (300 words) - 17:27, 30 July 2019
  • [ref2] J. C. Thomas, A. Van der Ven, Finite-temperature properties of strongly anharmon [ref4] A. Van der Ven, J. C. Thomas, Q. Xu, J. Bhattacharya “Linking the electronic structure of soli
    4 KB (453 words) - 13:20, 15 August 2022
  • ...J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annot
    4 KB (479 words) - 16:31, 27 May 2022
  • -c 25000 \
    1 KB (194 words) - 13:23, 6 June 2022
  • ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many" ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many"
    3 KB (590 words) - 16:53, 18 May 2022
  • ...Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation progra ...-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (20
    5 KB (763 words) - 12:39, 12 August 2022
  • James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Eliza
    2 KB (249 words) - 17:04, 6 September 2017
  • ...eate as many terminal windows in the screen session as needed with 'Ctrl+a c' key combination. See [[Screen]] documentation. Ctrl+a c
    4 KB (701 words) - 15:51, 9 July 2020
  • Fastest Fourier Transform in the West, is a C library for computing the Discrete Fourier Transform (DFT) in one or more d
    2 KB (223 words) - 16:41, 15 August 2022
  • Mach2VCF is a C++ tool to convert MaCH files to VCF files.
    2 KB (242 words) - 14:49, 10 June 2022
  • Validation suite for Variant Call Format (VCF) files, implemented using C++11
    2 KB (247 words) - 21:29, 6 December 2019
  • ...loped by Facebook AI Research Lab and has interfaces for Python, Java, and C++, but is most commonly used with Python. It supports training on both GPU ...-GPU and distributed training. APIs are available for Python, Java, Go and C++. See our [[TensorFlow|TensorFlow quickstart page]] for help getting start
    4 KB (584 words) - 18:44, 16 August 2022
  • DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther format
    2 KB (252 words) - 15:04, 10 June 2022
  • SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
    2 KB (247 words) - 17:47, 22 September 2021
  • OpenSlide is a C library that provides a simple interface to read whole-slide images
    2 KB (248 words) - 21:22, 6 December 2019
  • ...arch Computing. To run CellProfiler in batch mode, you should include the -c or --run-headless option. Also, you want to use CELLPROFILER_USE_XVFB="1" -c, --run-headless Run headless (without the GUI)
    8 KB (889 words) - 13:24, 15 August 2022
  • ...family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL).
    2 KB (251 words) - 14:57, 12 August 2022
  • Widely used C++ template library for task parallelism.
    2 KB (259 words) - 21:29, 6 December 2019
  • TALESF is a C library for identifying potential binding sites for transcription activator
    2 KB (256 words) - 21:29, 6 December 2019
  • ...e fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
    2 KB (256 words) - 15:23, 15 August 2022
  • C++ implementation of the Google logging module
    2 KB (269 words) - 17:10, 15 August 2022
  • C++ library and its applications to generate and process accurate consensus s
    2 KB (268 words) - 17:48, 15 August 2022
  • ...nome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
    2 KB (266 words) - 18:58, 12 August 2022
  • Networks. It is a C++ template library providing efficient implementations
    2 KB (268 words) - 15:41, 6 June 2022
  • ...t provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
    2 KB (269 words) - 15:49, 10 June 2022
  • IGoR is a C++ software designed to infer V(D)J recombination related processes from seq
    2 KB (271 words) - 13:52, 14 May 2020
  • ...s.biomedcentral.com/articles/10.1186/s12920-018-0342-1 Tony Kuo and Martin C Frith and Jun Sese and Paul Horton. EAGLE: Explicit Alternative Genome Like
    2 KB (270 words) - 22:30, 26 August 2020
  • ...oup.com/bioinformatics/article/31/16/2741/321286 Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. W
    2 KB (277 words) - 21:21, 6 December 2019
  • IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under
    2 KB (277 words) - 21:21, 6 December 2019
  • C. Than, D. Ruths, L. Nakhleh (2008) PhyloNet: A software package for analyzi
    2 KB (263 words) - 21:23, 6 December 2019
  • ...(MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
    2 KB (272 words) - 17:11, 15 August 2022
  • ...ead-safe, but, unlike MPFUN2020, is available with both a Fortran-90 and a C++ high-level interface.
    2 KB (271 words) - 17:47, 15 August 2022
  • QT is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language.
    2 KB (259 words) - 14:09, 13 June 2022
  • ...finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was develo
    2 KB (278 words) - 21:21, 6 December 2019
  • |{{#vardefine:app|netcdf-c}}
    2 KB (279 words) - 14:53, 3 June 2022
  • ...both functional and imperative paradigms. Rust is syntactically similar to C++, but its designers intend it to provide better memory safety while still
    2 KB (285 words) - 21:24, 6 December 2019
  • 1) a C library for units of physical quantities.
    2 KB (276 words) - 20:13, 10 June 2022
  • The ECMWF GRIB API is an application program interface accessible from C,
    2 KB (278 words) - 17:22, 15 August 2022
  • gui start -e gv -c 1 -m 8 -t 4 ...aramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G.
    7 KB (1,030 words) - 16:54, 15 August 2022
  • FastSpar is a c++ implementation of the SparCC algorithm published here: Friedman, J. & Alm
    2 KB (283 words) - 15:26, 15 August 2022
  • ...ble programs as well as several data structures and modules callable via a C API.
    2 KB (287 words) - 16:31, 10 June 2022
  • SNeP is a piece of software written in C++ that performs historical Effective Population Size (Ne) trajectories esti
    2 KB (278 words) - 16:23, 10 June 2022
  • rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The
    2 KB (289 words) - 19:26, 2 June 2022
  • The gflags package contains a C++ library that implements commandline flags processing. It includes built-i
    2 KB (291 words) - 17:07, 15 August 2022
  • rMATS turbo is the C/Cython version of rMATS (refer
    2 KB (292 words) - 18:14, 8 March 2022
  • and reliable geometric algorithms in the form of a C++ library.The Computational
    2 KB (293 words) - 15:32, 6 June 2022
  • ...i.nlm.nih.gov/pmc/articles/PMC5848618/ Tardaguila M, de la Fuente L, Marti C, et al. SQANTI: extensive characterization of long-read transcript sequence
    2 KB (290 words) - 20:35, 27 May 2022
  • ...plete Genomics data. The focus is to provide command line utilities, but a C++ API is available as well. The general areas of functionality include geno
    2 KB (291 words) - 13:26, 15 August 2022
  • ...rver. For edge deployments, Triton is available as a shared library with a C API that allows the full functionality of Triton to be included directly in
    2 KB (299 words) - 19:55, 1 June 2022
  • Blitz++ is a C++ class library for scientific computing which provides performance on par
    3 KB (303 words) - 21:19, 6 December 2019
  • CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexibl
    2 KB (291 words) - 13:26, 15 August 2022
  • Bgenix is a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software,
    2 KB (291 words) - 12:52, 15 August 2022
  • ..., J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgu
    3 KB (300 words) - 21:19, 6 December 2019
  • NCBI C++ Toolkit provides free, portable, public domain libraries with no restrict
    3 KB (306 words) - 17:47, 15 August 2022
  • ...and genotype frequencies from nucleotide read quartets (read counts of A, C, G, and T) derived from individual high-throughput sequencing data for mult
    2 KB (280 words) - 16:45, 10 June 2022
  • ...plementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime. A growing family of solutions and an acti
    2 KB (289 words) - 17:41, 15 August 2022
  • PhiSpy is a computer program written in C++, Python and R to identify prophages in a complete bacterial genome sequen
    2 KB (291 words) - 21:23, 6 December 2019
  • C++ and is open source.
    3 KB (302 words) - 16:49, 10 June 2022
  • BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM
    2 KB (289 words) - 18:02, 12 August 2022
  • Sputnik is a C language program that searches dna sequence files in Fasta format for micro
    2 KB (313 words) - 20:44, 12 August 2022
  • Chan chan PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter,
    2 KB (298 words) - 18:11, 15 April 2020
  • [https://www.nature.com/articles/ncomms14061 Jeffares, Daniel C; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampo
    3 KB (296 words) - 21:24, 6 December 2019
  • ...ls (MSMs). It is primarily written in the python programming language with C extensions for the most time consuming routines. MSMs are a powerful means
    2 KB (288 words) - 16:38, 10 June 2022
  • Baron RV, Kollar C, Mukhopadhyay N, Weeks DE (2014) Mega2: validated data-reformatting for lin
    3 KB (310 words) - 21:21, 6 December 2019
  • The MPFR library is a C library for multiple-precision floating-point computations with correct rou
    2 KB (302 words) - 21:22, 6 December 2019
  • Mitsuba 2 is a research-oriented rendering system written in portable C++17. It consists of a small set of core libraries and a wide variety of plu
    3 KB (300 words) - 19:42, 3 June 2022
  • Written in C++ and built on the Armadillo linear algebra library, the ensmallen numerica
    3 KB (301 words) - 19:43, 15 December 2020
  • ControlPath ~/.ssh/control/%C
    2 KB (310 words) - 20:15, 2 May 2022
  • [https://www.ncbi.nlm.nih.gov/pubmed/29718191 Oh, M., Pruden, A., Chen, C., Heath, L. S., Xia, K., & Zhang, L. (2018). MetaCompare: A computational p
    3 KB (304 words) - 21:21, 6 December 2019
  • Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and m
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  • ...models into efficient finite element code. With the high-level Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS offers also p
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  • ...ult to use? In G. Bertorelle, M. W. Bruford, H. C. Hauffe, A. Rizzoli, and C. Vernesi, editors, Population Genetics for Animal Conservation, volume 17 o
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  • ...1/1755-0998.12399/abstract Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and T
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  • LZO is a portable lossless data compression library written in ANSI C.
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  • AD Model Builder, or ADMB, is a C++ application which implements AD using specialized classes and operator ov
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  • software. The current version provides a complete BLAS API (for both C and
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  • ...reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.
    3 KB (320 words) - 17:17, 10 June 2022
  • ...aMiner must be present in your configure.txt file (which is passed by the -c option when you run decontaMiner.sh). In order to use the pre-loaded tools
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  • ...solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR
    3 KB (314 words) - 20:12, 8 February 2021
  • ...est.github.io/papers/BursteddeWilcoxGhattas11.pdf Carsten Burstedde, Lucas C. Wilcox, and Omar Ghattas, p4est: Scalable Algorithms for Parallel Adaptive
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  • [http://dl.acm.org/citation.cfm?id=2834999 C. Rosales, A. Gómez-Iglesias, A. Predoehl. "REMORA: a Resource Monitoring T
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  • ...formatics/article/36/17/4658/5861530 César Piñeiro, José M. Abuín and Juan C. Pichel. Bioinformatics, vol. 36, no. 17, pages 4658-4659, 2020.]
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  • ...ology 2014, and Evolution 2015). BAMM is a command line program written in C++. Post-run analysis and visualization is performed using the R package BAM
    3 KB (322 words) - 18:00, 12 August 2022
  • ...felt, R. Tabbara, T. Dhollander, M. Pietsch, D. Christiaens, B. Jeurissen, C.-H. Yeh, and A. Connelly. MRtrix3: A fast, flexible and open software frame
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  • compile $(CC) -c yourfile.c and link with $(CLINKER) -o yourprog
    3 KB (356 words) - 17:28, 10 June 2022
  • ...e discarding the rest. To write a program to do this in a language such as C or Pascal is a time-consuming inconvenience that may take many lines of cod
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  • ...id=10.1371/journal.pone.0174250 Philippon H., Souvane A., Brochier-Armanet C. and Perrière, G. (2017) IsoSel: Protein Isoform Selector for Phylogenetic
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  • launch_tgicl tgicl -F sample.fasta -q sample.qual -c 4
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  • Finesse is written in C and is compiled into a single binary executable called 'kat'. Today the pre
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  • Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic
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  • .../journals.plos.org/plosone/article?id=10.1371/journal.pone.0209523 Herzeel C, Costanza P, Decap D, Fostier J, Verachtert W (2019) elPrep 4: A multithrea
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  • * M. F. Rogers, C. Boucher, A. Ben-Hur. SpliceGrapherXT: from splice graphs to transcripts us
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  • components implemented in Python and C++ (With Python bindings).
    3 KB (357 words) - 17:03, 6 June 2022
  • ...5-018-2976-9 Ma, W., Qiu, Z., Song, J., Li, J., Cheng, Q., Zhai, J., & Ma, C. (2018). A deep convolutional neural network approach for predicting phenot
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  • ...exposes a set of carefully selected data structures and algorithms in both C++ and Python. The backend is highly optimized and is set up for paralleliza
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  • sequel -c sample.fasta -ap reads_aln.sam -i 404
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  • ...CH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequ
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  • Lorenzi, C., Barriere, S., Villemin, J. et al. iMOKA: k-mer based software to analyze
    3 KB (346 words) - 17:07, 27 May 2022
  • $ gui start -e rstudio -c 2 -m 8 -t 24 $ gui start --module fsl/6.0.3 -e fsleyes -c 2 -m 8 -t 24
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  • ...making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
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  • ...ing NumPy arrays. Other, less well-typed code will be translated to Python C-API calls effectively removing the "interpreter" but not removing the dynam
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  • ...dner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C, and Wickett, N. J. (2016). HybPiper: Extracting Coding Sequence and Intron
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  • ...much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed
    3 KB (349 words) - 20:53, 12 August 2022
  • Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS. (2011). Nipype: a flexible, li
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  • The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library co
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  • * dynamic C code generation – Evaluate expressions faster.
    3 KB (345 words) - 15:58, 6 June 2022
  • ...gart G, Schwarzberg Lipson K, Knight R, Caporaso JG, Segata N, Huttenhower C. Species-level functional profiling of metagenomes and metatranscriptomes.
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  • | Linear regr. over a 3000x3000 matrix (c = a \ b') || 12.57 || 5.92 || 1.37 || 0.41
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  • CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the
    3 KB (375 words) - 18:43, 10 June 2022
  • ...biomedcentral.com/articles/10.1186/s13059-014-0573-1 Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable J, Schnable P, Lyons E, Lu J. (2015) ALLMAPS: ro
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  • ...rary_effective_population_size_Ne_from_genetic_data_Mol_Ecol_Resour_14 Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J. & Ovenden, J. R.
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  • ...specially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes.
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  • ...mming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) a
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  • [I 15:38:38.859 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 15:38:38.862 NotebookApp]
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  • ...sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software
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  • ...Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. Journal of Antimicrobial Chemotherapy. 2020 Aug 11.
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  • ...D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk,
    3 KB (360 words) - 20:55, 12 August 2022
  • ...rect.com/science/article/pii/S0042682216303166 Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling K-S, Kreuze J, Fei Z (2017) V
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  • c. Click on transfer. * You can save data in the default C:\ drive, but it will be wiped out at the end of every session, so creating
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  • ...interacting with ROOT in Python should not feel like you are still writing C++.
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  • ...for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.
    3 KB (395 words) - 15:19, 15 August 2022
  • ...hed work, please include a reference to my PeerJ article: Moller AG, Liang C. (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unass
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  • ...rticles/10.1186/s40168-015-0093-6 Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M. Tiedje and J. R. Cole. Xander: Employing a Novel Method fo
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  • AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) da
    3 KB (363 words) - 20:52, 11 August 2022
  • ...er, Emma Schwager,Jason Lloyd-Price, George Weingart, Yo Sup Moon, Xochitl C. Morgan, Levi Waldron, Eric A. Franzosa, Curtis Huttenhower. High-sensitivi
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  • [https://www.ncbi.nlm.nih.gov/pubmed/25609793 Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast sin
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  • The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and compar
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  • [1] Neigenfind J1, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozy
    3 KB (344 words) - 19:11, 10 June 2022
  • Zhang, C. †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013. Prediction of clus
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  • ...orithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed.
    3 KB (389 words) - 20:53, 12 August 2022
  • ...h, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatom
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  • Gblocks is a computer program written in ANSI C language that eliminates
    3 KB (441 words) - 13:56, 13 June 2022
  • Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.
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  • Quit the server with CONTROL-C.
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  • ...ge-scale sequence analysis and is now available in terms of an open source C library. UProC is up to three orders of magnitude faster than profile-based
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  • gem5 is written primarily in C++ and python and most components are provided under a BSD style license. It
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  • SAMStat is an efficient C program to quickly display statistics of large sequence files from next gen
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  • #Looks good, let's terminate the request with Ctrl+C> ^C
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  • Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing
    3 KB (452 words) - 19:26, 10 June 2022
  • ...r the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART
    3 KB (440 words) - 21:10, 6 December 2019
  • ...rees by maximizing a pseudo-likelihood function. The program is written in C. The parallel version of the program can run independent searches (chains)
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  • :: Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It use
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  • ...taxonomic profiling of NGS libraries has been developed as a collection of C++, Perl and R scripts.
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  • Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E.
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  • Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of
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  • Marçais, G. and C. Kingsford. 2011. A fast, lock-free approach for efficient parallel countin
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  • ...written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal
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  • ...ng problems faster than with traditional programming languages, such as C, C++, and Fortran. -rw-r--r-- 1 root root 2900 Apr 3 10:08 houdini_main.c
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  • java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10
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  • ...oad the environment module and run <code>pip3 list</code> or <code>python -c "help('modules')"</code> command before submitting a request for a new modu
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  • sinfo -o %P,%D,%c,%X,%m,%f
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  • ...lick on the MobaXTerm terminal where you started the command and use 'Ctrl+c" key combination to detach from the session, so you could re-attach later.
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  • * Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation o * Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATé-II: Very Fast and Accurate Simultaneous Estimation of Mul
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  • #M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:7 #M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data
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  • ...dia CUDA Toolkit]] page. The current CUDA environment is cuda/11. However, C++ or Python packages numba and PyCuda are other ways to program GPU algorit
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  • *<code>-c, --cpus-per-task=<ncpus></code>
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  • <code>mamba install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch</code>
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  • FC="mpif90 -c" \ FC="mpif90 -c" \
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