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  • Ngsremix
    The method is implemented as a C/C++ commandline program.
    2 KB (259 words) - 21:49, 28 February 2023
  • Dlib
    ...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
  • Armadillo
    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
  • SALSA
    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 (269 words) - 20:11, 24 August 2022
  • SUNDIALS
    ...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 (364 words) - 15:25, 19 August 2022
  • ImageMagick
    ...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
  • C-wap
    |{{#vardefine:app|c-wap}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/C-WAP}}
    2 KB (281 words) - 13:16, 15 August 2022
  • GRACKLE
    ...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
    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
  • Panaroo
    ...dair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. 2020. Producing p
    2 KB (289 words) - 19:33, 13 June 2023
  • Deepfri
    ...ek, T., Leman, J. K., Berenberg, D., Vatanen, T., Chandler, C., Taylor, B. C., Fisk, I. M., Vlamakis, H., Xavier, R. J., Knight, R., Cho, K., & Bonneau,
    2 KB (290 words) - 19:30, 10 March 2023
  • Plinkseq
    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
  • HOOMD
    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
  • NetCDF
    ...e that the Fortran module man not have all supporting binaries that netcdf-c module has.
    3 KB (402 words) - 14:56, 12 March 2024
  • GSL
    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
  • OpenCV
    ...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
  • Quantisnp
    ...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
  • GEOS
    ...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
  • DCMTK
    ...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
    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
  • TAU
    ...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 (581 words) - 22:37, 24 October 2022
  • Segemehl
    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 (406 words) - 22:30, 21 August 2022
  • GDSL
    ...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
  • Imagej2
    Rueden, C. T., Schindelin, J., Hiner, M. C., DeZonia, B. E., Walter, A. E., Arena, E. T., & Eliceiri, K. W. (2017). Im
    3 KB (308 words) - 16:31, 20 October 2022
  • Allhic
    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
  • KIM
    * C * C++
    3 KB (322 words) - 19:19, 15 August 2022
  • Intel Compilers and Libraries
    | C || icc || ''icc compiler_options example.c'' | C++ || icpc || ''icpc compiler_options -o example.exe example.cxx''
    5 KB (612 words) - 18:04, 27 September 2023
  • 3d-dna
    ...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
  • Minimac
    ...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) - 20:11, 18 August 2022
  • OpenCL
    ...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 (365 words) - 17:52, 19 August 2022
  • SHARCGS
    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 (313 words) - 22:42, 21 August 2022
  • PICRUSt
    ...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
  • HOMER
    ...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
  • Maq
    maqindex -i -c consensus.cns all.map; maqview -c consensus.cns all.map
    3 KB (377 words) - 19:47, 12 August 2022
  • Phenix
    .... 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 (325 words) - 18:12, 21 August 2022
  • Biolite
    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
  • BUCKy
    [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
    ...Elastix, making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.
    3 KB (365 words) - 15:30, 3 June 2022
  • Mamba
    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
  • Genesis
    1. C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, 2. J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, WIREs Comput. Mo
    3 KB (368 words) - 17:51, 3 April 2024
  • ChartDirector
    VBScript, VBA, JavaScript, .NET (C#/VB), Java, JSP, C++, PHP, Perl, Python,
    3 KB (397 words) - 13:26, 15 August 2022
  • USEARCH
    Edgar, Robert C. - Search and clustering orders of magnitude faster than BLAST Author : Edgar, Robert C.
    4 KB (559 words) - 17:19, 22 August 2022
  • PICSL
    [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) - 20:31, 24 August 2022
  • SLURM Environmental Variables
    ...Number of cores per task. I.e., the value given to the -cpus-per-task or -c sbatch options. Not set unless one of those options given.
    1 KB (236 words) - 17:43, 5 March 2024
  • CASM
    [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
  • EDTA
    ...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 (474 words) - 21:27, 14 September 2023
  • LAMMPS
    ...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
    5 KB (731 words) - 20:30, 6 April 2024
  • Account and QOS limits under SLURM
    #Looks good, let's terminate the request with Ctrl+C> ^C
    8 KB (1,354 words) - 18:36, 9 February 2024
  • AMBER
    ...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 (736 words) - 20:09, 5 February 2024
  • Tensorboard
    ...orBoard 2.4.0 at '''<nowiki>http://localhost:6006/</nowiki>''' (Press CTRL-C to quit)
    2 KB (231 words) - 21:03, 12 December 2023

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