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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 (278 words) - 14:47, 19 August 2022
- NCBI C++ Toolkit provides free, portable, public domain libraries with no restrict3 KB (306 words) - 14:25, 19 August 2022
File:2012-04-19-Parallel Processing-C Taylor.ppt (1.42 MB) - 16:10, 19 April 2012
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- ...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.24 members (0 subcategories, 0 files) - 17:51, 27 September 2023
- mpicc ( C source) mpiCC (C++ source)3 KB (297 words) - 12:01, 26 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-e3 KB (414 words) - 20:04, 21 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-x3 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 u3 KB (350 words) - 13:06, 15 August 2022
- |{{#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 st3 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
- a) module load intel/2020.0.166 openmpi/4.1.5 netcdf-c/4.9.2 netcdf-f/4.6.1 metis/5.2.1 cmake/3.26.4 petsc/3.19.4 ...export NETCDF_CFLAGS="-I/apps/intel/2020.0.166/openmpi/4.1.5/netcdf-c/4.9.2/include\2 KB (310 words) - 14:05, 17 April 2024
- Type: <code>ssh-keygen -t ed25519 -C "My HiPerGator Key"</code> C:\> ssh-keygen -t ed25519 -C "My HiPerGator Key"4 KB (634 words) - 17:53, 12 September 2023
- 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.inpcrd1 KB (171 words) - 21:18, 5 December 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 5:12 KB (276 words) - 16:49, 15 August 2022
- |{{#vardefine:url|https://fan-c.readthedocs.io/}} FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.2 KB (281 words) - 15:56, 22 March 2024
- ...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 (libs2 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 and3 KB (406 words) - 14:47, 15 August 2022
- ...GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC® directives, and CUDA®. GPU-accelerated math libra3 KB (334 words) - 17:24, 19 August 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. 203 KB (329 words) - 21:22, 6 December 2019
- ...stq raw data files and command line tools for feature annotation on the Hi-C maps. The juicer pipeline submits jobs to the cluster and then exits. It ca3 KB (369 words) - 16:29, 15 October 2023
- The method is implemented as a C/C++ commandline program.2 KB (259 words) - 21:49, 28 February 2023
- ...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 do2 KB (269 words) - 13:11, 4 May 2020
- 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 Intensive2 KB (269 words) - 14:33, 12 August 2022
- 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 in2 KB (269 words) - 20:11, 24 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," Proce3 KB (364 words) - 15:25, 19 August 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
- ...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
- ...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 p2 KB (289 words) - 19:33, 13 June 2023
- ...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
- PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus2 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 simulations5 KB (607 words) - 15:40, 6 June 2022
- ...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
- The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General2 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 Op2 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 de2 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 predica3 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 o3 KB (303 words) - 20:08, 31 May 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 A4 KB (581 words) - 22:37, 24 October 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, H3 KB (406 words) - 22:30, 21 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 imp3 KB (305 words) - 15:37, 6 June 2022
- Rueden, C. T., Schindelin, J., Hiner, M. C., DeZonia, B. E., Walter, A. E., Arena, E. T., & Eliceiri, K. W. (2017). Im3 KB (308 words) - 16:31, 20 October 2022
- 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
- | 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
- ...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 ahea3 KB (328 words) - 17:51, 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 imputa3 KB (332 words) - 20:11, 18 August 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.c3 KB (365 words) - 17:52, 19 August 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 sets3 KB (313 words) - 22:42, 21 August 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
- maqindex -i -c consensus.cns all.map; maqview -c consensus.cns all.map3 KB (377 words) - 19:47, 12 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 (325 words) - 18:12, 21 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 files3 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 Bayes3 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
- Mamba is a reimplementation of the conda package manager in C++. core parts of mamba are implemented in C++ for maximum efficiency3 KB (429 words) - 20:16, 3 June 2022
- 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. Mo3 KB (368 words) - 17:51, 3 April 2024
- 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 (559 words) - 17:19, 22 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) - 20:31, 24 August 2022
- ...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
- [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 soli4 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 Annot4 KB (474 words) - 21:27, 14 September 2023
- ...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 ../cmake5 KB (731 words) - 20:30, 6 April 2024
- #Looks good, let's terminate the request with Ctrl+C> ^C8 KB (1,354 words) - 18:36, 9 February 2024
- ...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 (205 KB (736 words) - 20:09, 5 February 2024
- ...orBoard 2.4.0 at '''<nowiki>http://localhost:6006/</nowiki>''' (Press CTRL-C to quit)2 KB (231 words) - 21:03, 12 December 2023
- ===cuda_bm.c=== {{#fileAnchor: cuda_bm.c}}12 KB (1,540 words) - 17:09, 21 December 2022
- c) Copy remote e/n/d/r/c/s/q> n6 KB (763 words) - 20:07, 30 October 2023
- ...eate as many terminal windows in the screen session as needed with 'Ctrl+a c' key combination. See [[Screen]] documentation. Ctrl+a c4 KB (719 words) - 13:36, 2 January 2023
- Fastest Fourier Transform in the West, is a C library for computing the Discrete Fourier Transform (DFT) in one or more d2 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++112 KB (249 words) - 17:27, 22 August 2022
- DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther format2 KB (252 words) - 15:04, 10 June 2022
- SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.2 KB (247 words) - 17:57, 19 August 2022
- OpenSlide is a C library that provides a simple interface to read whole-slide images2 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 (910 words) - 21:29, 21 December 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 activator2 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 module2 KB (269 words) - 17:10, 15 August 2022
- C++ library and its applications to generate and process accurate consensus s2 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 implementations2 KB (268 words) - 15:41, 6 June 2022
- ...family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL).2 KB (267 words) - 17:50, 28 August 2023
- ...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 seq2 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 Like2 KB (270 words) - 22:30, 26 August 2020
- QT is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language.2 KB (257 words) - 20:57, 21 August 2022
- ...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. W2 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 under2 KB (277 words) - 21:21, 6 December 2019
- C. Than, D. Ruths, L. Nakhleh (2008) PhyloNet: A software package for analyzi2 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
- Savojardo C., Martelli P.L., Fariselli P., Casadio R. DeepSig: deep learning improves s2 KB (266 words) - 04:24, 6 December 2022
- |{{#vardefine:app|netcdf-c}}2 KB (278 words) - 14:47, 19 August 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 develo2 KB (278 words) - 21:21, 6 December 2019
- ...both functional and imperative paradigms. Rust is syntactically similar to C++, but its designers intend it to provide better memory safety while still2 KB (285 words) - 21:24, 6 December 2019
- The ECMWF GRIB API is an application program interface accessible from C,2 KB (278 words) - 17:22, 15 August 2022
- FastSpar is a c++ implementation of the SparCC algorithm published here: Friedman, J. & Alm2 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 esti2 KB (278 words) - 16:23, 10 June 2022
- 1) a C library for units of physical quantities.2 KB (279 words) - 17:17, 22 August 2022
- rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The2 KB (289 words) - 19:26, 2 June 2022
- The gflags package contains a C++ library that implements commandline flags processing. It includes built-i2 KB (291 words) - 17:07, 15 August 2022
- rMATS turbo is the C/Cython version of rMATS (refer2 KB (292 words) - 18:14, 8 March 2022
- and reliable geometric algorithms in the form of a C++ library.The Computational2 KB (293 words) - 15:32, 6 June 2022
- **<pre>gui start -e gv -c 1 -m 8 -t 4</pre>2 KB (341 words) - 19:17, 25 January 2023
- ...i.nlm.nih.gov/pmc/articles/PMC5848618/ Tardaguila M, de la Fuente L, Marti C, et al. SQANTI: extensive characterization of long-read transcript sequence2 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 geno2 KB (291 words) - 13:26, 15 August 2022
- Blitz++ is a C++ class library for scientific computing which provides performance on par3 KB (303 words) - 21:19, 6 December 2019
- ...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 in2 KB (298 words) - 20:06, 21 August 2022
- CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexibl2 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
- NCBI C++ Toolkit provides free, portable, public domain libraries with no restrict3 KB (306 words) - 14:25, 19 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 shotgu3 KB (300 words) - 21:19, 6 December 2019
- ...and genotype frequencies from nucleotide read quartets (read counts of A, C, G, and T) derived from individual high-throughput sequencing data for mult2 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 acti2 KB (289 words) - 17:41, 15 August 2022
- Sputnik is a C language program that searches dna sequence files in Fasta format for micro2 KB (311 words) - 15:50, 22 August 2022
- PhiSpy is a computer program written in C++, Python and R to identify prophages in a complete bacterial genome sequen2 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 BAM2 KB (289 words) - 18:02, 12 August 2022
- James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Eliza2 KB (245 words) - 13:45, 19 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, Charalampo3 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 means2 KB (288 words) - 16:38, 10 June 2022
- Baron RV, Kollar C, Mukhopadhyay N, Weeks DE (2014) Mega2: validated data-reformatting for lin3 KB (310 words) - 21:21, 6 December 2019
- The MPFR library is a C library for multiple-precision floating-point computations with correct rou2 KB (302 words) - 21:22, 6 December 2019
- Written in C++ and built on the Armadillo linear algebra library, the ensmallen numerica3 KB (301 words) - 19:43, 15 December 2020
- [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 p3 KB (304 words) - 21:21, 6 December 2019
- Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and m2 KB (296 words) - 20:22, 12 August 2022
- ...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 p3 KB (301 words) - 21:20, 6 December 2019
- isONclust2 is implemented in C++, which makes it fast enough to cluster large transcriptomic datasets prod3 KB (303 words) - 15:23, 28 October 2022
- 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 plu3 KB (302 words) - 20:45, 18 August 2022
- ...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 o5 KB (636 words) - 16:05, 22 December 2022
- ...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.6 KB (918 words) - 14:39, 8 March 2023
- ...1/1755-0998.12399/abstract Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and T3 KB (300 words) - 19:29, 18 August 2022
- LZO is a portable lossless data compression library written in ANSI C.3 KB (317 words) - 20:38, 10 June 2022
- ...' (or '''B'''iosynthetic '''G'''ene clusters - '''S'''uper '''Li'''near '''C'''lustering '''E'''ngine) is a tool designed to cluster massive numbers of3 KB (295 words) - 21:25, 14 September 2023
- AD Model Builder, or ADMB, is a C++ application which implements AD using specialized classes and operator ov3 KB (302 words) - 20:49, 11 August 2022
- software. The current version provides a complete BLAS API (for both C and3 KB (317 words) - 15:19, 12 August 2022
- ...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 tools3 KB (321 words) - 14:56, 2 March 2021
- ...solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3 KB (314 words) - 20:12, 8 February 2021
- ControlPath ~/.ssh/control/%C2 KB (342 words) - 13:40, 26 June 2023
- ...est.github.io/papers/BursteddeWilcoxGhattas11.pdf Carsten Burstedde, Lucas C. Wilcox, and Omar Ghattas, p4est: Scalable Algorithms for Parallel Adaptive3 KB (320 words) - 17:24, 10 June 2022
- ...formatics/article/36/17/4658/5861530 César Piñeiro, José M. Abuín and Juan C. Pichel. Bioinformatics, vol. 36, no. 17, pages 4658-4659, 2020.]3 KB (329 words) - 21:03, 12 February 2021
- ...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 BAM3 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 frame3 KB (311 words) - 20:34, 24 August 2022
- ...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 mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch5 KB (767 words) - 20:15, 16 April 2024
- emeraLD v0.1 (c) 2018 corbin quick (corbinq@gmail.com)3 KB (324 words) - 19:16, 29 October 2023
- compile $(CC) -c yourfile.c and link with $(CLINKER) -o yourprog3 KB (356 words) - 17:28, 10 June 2022
- [http://dl.acm.org/citation.cfm?id=2834999 C. Rosales, A. Gómez-Iglesias, A. Predoehl. "REMORA: a Resource Monitoring T3 KB (330 words) - 20:39, 24 August 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 cod3 KB (356 words) - 16:55, 15 August 2022
- ...id=10.1371/journal.pone.0174250 Philippon H., Souvane A., Brochier-Armanet C. and Perrière, G. (2017) IsoSel: Protein Isoform Selector for Phylogenetic3 KB (345 words) - 14:29, 26 March 2021
- launch_tgicl tgicl -F sample.fasta -q sample.qual -c 43 KB (340 words) - 20:47, 12 August 2022
- Finesse is written in C and is compiled into a single binary executable called 'kat'. Today the pre3 KB (347 words) - 00:01, 9 July 2020
- ...hua Zeng, Brian Williams, Diane Trout, Whitney England, Sophie Chu, Robert C. Spitale, Andrea J. Tenner, Barbara J. Wold, Ali Mortazavi bioRxiv 672931;3 KB (321 words) - 15:13, 23 September 2022
- Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic3 KB (340 words) - 17:48, 10 June 2022
- .../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 multithrea3 KB (345 words) - 21:20, 6 December 2019
- * M. F. Rogers, C. Boucher, A. Ben-Hur. SpliceGrapherXT: from splice graphs to transcripts us3 KB (318 words) - 21:24, 6 December 2019
- ...chal Babinski, Yan Xu, Bin Hu, Patrick S. G. Chain, Stephen Nayfach, Nikos C. Kyrpides bioRxiv 2023.03.05.531206; doi: https://doi.org/10.1101/2023.03.03 KB (332 words) - 13:25, 7 April 2023
- 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 phenot3 KB (342 words) - 22:21, 26 August 2020
- [https://doi.org/10.1093/bioinformatics/btae042 Holt, J. M., Saunders, C. T., Rowell, W. J., Kronenberg, Z., Wenger, A. M., & Eberle, M. (2024). HiP3 KB (337 words) - 20:21, 19 March 2024
- ...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 start6 KB (870 words) - 17:17, 22 April 2024
- ...CH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequ3 KB (349 words) - 19:36, 21 August 2022
- Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation.3 KB (337 words) - 15:42, 6 September 2022
- Lorenzi, C., Barriere, S., Villemin, J. et al. iMOKA: k-mer based software to analyze3 KB (346 words) - 17:07, 27 May 2022
- ...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 3.3 KB (334 words) - 12:56, 15 August 2022
- sequel -c sample.fasta -ap reads_aln.sam -i 4043 KB (382 words) - 22:39, 21 August 2022
- ...ing NumPy arrays. Other, less well-typed code will be translated to Python C-API calls effectively removing the "interpreter" but not removing the dynam3 KB (353 words) - 20:44, 15 August 2022
- ...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 Intron3 KB (349 words) - 18:36, 10 June 2022
- ...much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed3 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, li3 KB (348 words) - 20:07, 12 August 2022
- The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library co3 KB (350 words) - 17:47, 15 August 2022
- * 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.3 KB (348 words) - 22:26, 27 August 2020
- Deneke, C.; Brendebach, H.; Uelze, L.; Borowiak, M.; Malorny, B.; Tausch, S.H.3 KB (348 words) - 22:07, 20 October 2023
- | Linear regr. over a 3000x3000 matrix (c = a \ b') || 12.57 || 5.92 || 1.37 || 0.412 KB (216 words) - 20:33, 15 August 2022
- CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the3 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: ro3 KB (361 words) - 21:11, 6 December 2019
- ...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.3 KB (375 words) - 19:56, 12 August 2022
- ...specially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes.3 KB (355 words) - 12:42, 12 August 2022
- ...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) a2 KB (341 words) - 19:35, 24 August 2022
- **<pre>ssh-keygen -o -a 100 -t ed25519 -f ~/.ssh/id_ed25519 -C "Comment to make the key recognizable among many"</pre> **<pre>ssh-keygen -t ed25519 -C "Comment to make the key recognizable among many"</pre>6 KB (1,087 words) - 18:54, 29 March 2024
- ...Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. Journal of Antimicrobial Chemotherapy. 2020 Aug 11.3 KB (342 words) - 18:41, 23 April 2021
- ...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) V3 KB (377 words) - 23:22, 30 July 2020
- ...interacting with ROOT in Python should not feel like you are still writing C++.3 KB (389 words) - 16:49, 21 August 2022
- ...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
- ...rs MPI enabled. At HiperGator we use OPENMPI. In addition, matching netcdf-c, netcdf-f and HDF5 modules must be present.3 KB (443 words) - 13:28, 27 March 2024
- ...tiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer. AnchorWave: Sensitive alignment of genomes with high sequence div3 KB (367 words) - 21:10, 20 September 2023
- $ PLASMe.py test.fasta test.plasme.fna -c 0.6 -i 0.6 -p 0.5 -t 83 KB (375 words) - 18:08, 3 April 2024
- ...hed work, please include a reference to my PeerJ article: Moller AG, Liang C. (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unass3 KB (392 words) - 17:58, 27 May 2022
- ...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 fo3 KB (381 words) - 19:07, 10 June 2022
- AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) da3 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-sensitivi3 KB (367 words) - 13:57, 25 March 2022
- C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Mar3 KB (360 words) - 14:04, 3 October 2022
- [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 sin3 KB (367 words) - 18:31, 18 August 2022
- The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and compar3 KB (396 words) - 19:08, 10 June 2022
- [1] Neigenfind J1, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozy3 KB (344 words) - 15:04, 19 August 2022
- #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 data3 KB (365 words) - 16:47, 17 January 2023
- # Use ''''Ctrl-C'''' key combination to stop the <code>tunnel</code> process. ...on requesting 4 cores, 15GB of RAM, an A100 GPU for 1 hour: <code>'''srun -c 4 --mem 15gb -p gpu --gres gpu:a100:1 -t 60 --pty bash -i'''</code>7 KB (1,100 words) - 17:42, 5 March 2024
- '''CSUBST''' is a tool for analyzing '''C'''ombinatorial '''SUBST'''itutions of codon sequences in phylogenetic trees3 KB (380 words) - 22:12, 26 July 2023
- Zhang, C. †, Lee, K.-Y., Swanson, M.S., Darnell, R.B. † 2013. Prediction of clus3 KB (399 words) - 14:53, 14 December 2022
- ...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 paralleliza3 KB (414 words) - 17:16, 7 July 2023
- ...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
- * Hi-C matrices (as triangle or squares)3 KB (375 words) - 20:54, 18 May 2023
- ...a dependency of the [https://github.com/ENCODE-DCC/hic-pipeline ENCODE Hi-C uniform processing pipeline]. Caper wraps Cromwell to run pipelines on mult3 KB (425 words) - 14:43, 11 October 2023
- ...h, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatom3 KB (397 words) - 19:23, 12 August 2022
- Gblocks is a computer program written in ANSI C language that eliminates3 KB (441 words) - 13:56, 13 June 2022
- mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch <code>mamba install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch</code>9 KB (1,496 words) - 16:52, 30 April 2024
- ...written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal3 KB (412 words) - 20:49, 21 October 2022
- Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.3 KB (378 words) - 14:53, 12 August 2022
- ...sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software3 KB (413 words) - 20:22, 2 October 2023
- Quit the server with CONTROL-C.3 KB (420 words) - 17:24, 22 August 2022
- ...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-based3 KB (418 words) - 20:53, 12 August 2022
- gem5 is written primarily in C++ and python and most components are provided under a BSD style license. It3 KB (434 words) - 19:23, 10 June 2022
- SAMStat is an efficient C program to quickly display statistics of large sequence files from next gen3 KB (429 words) - 20:34, 12 August 2022
- Deneke C, Uelze L, Brendebach H, Tausch SH and Malorny B (2021)4 KB (457 words) - 15:02, 23 October 2023
- ...r the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART3 KB (440 words) - 21:10, 6 December 2019
- ...cProfile for python code, [[Nsight]] Compute for CUDA apps, or VTune for C/C++ + MPI code.7 KB (1,199 words) - 02:11, 17 April 2024
- ...rees by maximizing a pseudo-likelihood function. The program is written in C. The parallel version of the program can run independent searches (chains)4 KB (489 words) - 12:01, 19 August 2022
- Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing3 KB (458 words) - 21:46, 21 August 2022
- :: Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It use4 KB (438 words) - 14:54, 15 August 2022
- ...taxonomic profiling of NGS libraries has been developed as a collection of C++, Perl and R scripts.4 KB (507 words) - 16:54, 14 December 2022
- Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of4 KB (474 words) - 21:23, 6 December 2019
- Marçais, G. and C. Kingsford. 2011. A fast, lock-free approach for efficient parallel countin4 KB (487 words) - 21:20, 6 December 2019
- ...mputing problems faster than traditional programming languages, such as C, C++, and Fortran. -rw-r--r-- 1 root root 2900 Apr 3 10:08 houdini_main.c9 KB (1,361 words) - 16:06, 28 November 2023
- sinfo -o %P,%D,%c,%X,%m,%f4 KB (574 words) - 15:30, 25 April 2024
- Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E.4 KB (556 words) - 19:16, 5 January 2023
- *<pre>java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10</pre>4 KB (562 words) - 15:19, 5 January 2023
- ...load the environment module and run <code>pip list</code> or <code>python -c "help('modules')"</code> command before submitting a request for a new modu5 KB (670 words) - 19:42, 3 February 2023
- -c 25000 \6 KB (774 words) - 14:28, 15 December 2022
- #* You can save data in the default C:\ drive, but it will be wiped out at the end of every session. Therefore, c6 KB (953 words) - 20:01, 18 July 2023
- * 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 Mul7 KB (910 words) - 20:43, 21 December 2022
- *<code>-c, --cpus-per-task=<ncpus></code>9 KB (1,347 words) - 19:05, 21 July 2023
- mamba install cudatoolkit=11.3 pytorch=1.12.1=gpu_cuda* -c pytorch16 KB (2,392 words) - 20:14, 16 April 2024
- FC="mpif90 -c" \ FC="mpif90 -c" \75 KB (8,369 words) - 08:47, 25 July 2013