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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
CUDA Examples
===cuda_bm.c=== {{#fileAnchor: cuda_bm.c}}

12 KB (1,540 words) - 17:09, 21 December 2022
Rclone
c) Copy remote e/n/d/r/c/s/q> n

6 KB (763 words) - 20:07, 30 October 2023
Persistent Terminal Sessions
...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 (719 words) - 13:36, 2 January 2023
FFTW
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
Mach2VCF is a C++ tool to convert MaCH files to VCF files.

2 KB (242 words) - 14:49, 10 June 2022
Vcf-validator
Validation suite for Variant Call Format (VCF) files, implemented using C++11

2 KB (249 words) - 17:27, 22 August 2022
DosageConvertor
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
OpenSim
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

2 KB (247 words) - 17:57, 19 August 2022
OpenSlide
OpenSlide is a C library that provides a simple interface to read whole-slide images

2 KB (248 words) - 21:22, 6 December 2019
CellProfiler
...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
Tbb
Widely used C++ template library for task parallelism.

2 KB (259 words) - 21:29, 6 December 2019
Talesf
TALESF is a C library for identifying potential binding sites for transcription activator

2 KB (256 words) - 21:29, 6 December 2019
Fastp
...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
Glog
C++ implementation of the Google logging module

2 KB (269 words) - 17:10, 15 August 2022
Unanimity
C++ library and its applications to generate and process accurate consensus s

2 KB (268 words) - 17:48, 15 August 2022
GenomeTools
...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
LEMON
Networks. It is a C++ template library providing efficient implementations

2 KB (268 words) - 15:41, 6 June 2022
Aster
...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
Libunistring
...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
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
Eagle-rc
...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
QT
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
MetaSV
...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
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
Phylonet
C. Than, D. Ruths, L. Nakhleh (2008) PhyloNet: A software package for analyzi

2 KB (263 words) - 21:23, 6 December 2019
GLPK
...(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
QD
...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
Deepsig
Savojardo C., Martelli P.L., Fariselli P., Casadio R. DeepSig: deep learning improves s

2 KB (266 words) - 04:24, 6 December 2022
NetCDF-C
|{{#vardefine:app|netcdf-c}}

2 KB (278 words) - 14:47, 19 August 2022
MiRanda
...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

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