Search Results for "cite" - Page 2
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Showing 206 open source projects for "cite"
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
...For a list of recent updates, visit: https://sourceforge.net/p/plateeditor/wiki/Updates/ Hoping PlateEditor will make your life easier in the lab! If yes, please cite us: https://doi.org/10.1371/journal.pone.0252488 -
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PH-NODE
Code for finding phonon nodes using first-principle approach.
...It is a density-functional perturbation theory and finite displacement supercell based software package for efficiently computing phonon nodes present in real material. The present version of the code is interfaced with the WIEN2k, Elk, and ABINIT packages. Please cite the paper mentioned below while using the PH-NODE code for your research. P. Pandey and S.K. Pandey, Comput. Phys. Commun. 303, 109281 (2024) The link of the paper: https://doi.org/10.1016/j.cpc.2024.109281 -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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affe
apple fruit feature extractor (affe)
The apple fruit features extractor (affe) is a tool for feature extraction in apple phenotyping under the GPL 3 license https://opensource.org/license/gpl-3-0 It works on data of the Fruitphenobox https://www.researchsquare.com/article/rs-2632704/v1 Developed and tested by Norbert Kirchgessner, ETH Zurich using Matlab 2018b as source code and compiled For the generation of fact sheets, some R skripts written by Marius Hodel, Agroscope Wädenswil, Switzerland, are included. If you find this project usefull, please cite Based on functions from the MatLib initiated at the Institute of Mechanobiology (IBI 2) of the Forschungszentrum Jülich GmbH (FZJ), https://www.fz-juelich.de/de/ibi/ibi-2 Sincere thanks to Prof. Dr. Rudolf Merkel (IBI2, FZJ) for granting the publication of MatLib functions and Prof. Dr. Sebastian Houben, Institute for Artificial Intelligence and Autonomous Systems (A2S), Bonn-Rhein-Sieg University of Applied Sciences, Germany for developing parts at FZJ -
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TRACK code
Code for finding the transport properties using Kubo formalism.
...It is possible to use the relaxation time approximation in this code with the eigenvalues of DFT method. In present version, the code is interfaced with WIEN2k and eDMFTF codes. Please cite the paper mentioned below while using the TRACK code for your research. A. Sihi and S. K. Pandey, Comput. Phys. Commun. 285, 108640 (2023). Link of the paper: https://doi.org/10.1016/j.cpc.2022.108640 -
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Weinberg-R2R
Faster creation of aesthetic RNA secondary structure diagrams
...R2R is freely available under the GNU Public License, and runs as a command-line program under UNIX-like systems such as Linux, MacOS Darwin or Cygwin on Windows. R2R was written by Zasha Weinberg. If you use it, please cite this paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-3 -
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
...Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ, please cite this preprint: 123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads https://www.biorxiv.org/content/10.1101/2024.03.08.584032v1 ########################################################## Take care of the details and ensure you use the latest version. We hope this helps... -
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Habfuzz
A command-line tool for data-driven fuzzy modelling
Input 1 - A training dataset (multiple observations) of up to four variables (predictors) against one (response variable) Input 2 - A test dataset (multiple observations) of the same four variables with unknown response variable Output - Calculation of the response variable for each test observation using fuzzy logic or fuzzy rule-based Bayesian algorithms HABFUZZ is a habitat model, which can be used in ecohydraulic modelling applications for the calculation of the instream habitat... -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
...It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
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Alphafold
Open source code for AlphaFold
...For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from using this source code or the model parameters should cite the AlphaFold paper. Please also refer to the Supplementary Information for a detailed description of the method. You can use a slightly simplified version of AlphaFold with this Colab notebook or community-supported versions. The total download size for the full databases is around 415 GB and the total size when unzipped is 2.2 TB. ... -
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Citar
Emacs package to quickly find and act on bibliographic references
...Citar provides a highly configurable completing-read front-end to browse and act on BibTeX, BibLaTeX, and CSL JSON bibliographic data, and LaTeX, markdown, and org-cite editing support. -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1. Vengadesan, K. & Gautham, N. Enhanced sampling of the molecular potential energy surface using mutually orthogonal Latin squares: Application to peptide structures. ...
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BD-Func
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159 -
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PY-Nodes
Code for finding nodes in a material using first-principle approach.
...The algorithm of the code is based on the Nelder-Mead’s function-minimization approach. The code minimizes the function f(k), which is defined as sum of the absolute energy difference of the adjacent pairs of bands at a given k-point. Please cite the paper mentioned below while using the PY-Nodes code for your research. V. Pandey and S.K. Pandey, Comput. Phys. Commun. 283, 108570 (2023). The link of the paper: https://doi.org/10.1016/j.cpc.2022.108570 -
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* To cite this dataset refer to http://dx.doi.org/10.12785/ijcds/130177 Mazari, A. C., & Kheddar, H. (2023). "Deep Learning-based Analysis of Algerian Dialect Dataset Targeted Hate Speech, Offensive Language and Cyberbullying." IJCDS, 13(1). * Due to the nature of this Dataset, comments contain offensiveness and hate speech.
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Sentiment dataset of Algerian dialect
Dataset of 11760 sentiment comments written in Algerian dialect
* To cite this dataset refer to https://doi.org/10.31449/inf.v46i6.3340 * This sentiment dataset of Algerian dialect consists of 11760 comments (6111 positive/ 5649 negative comments)) collected from (Facebook, YouTube and Twitter) during Hirak 2019. * Comments concern the Algerian spoken language, written in Arabic and/or Latin characters and/or Arabizi, which could be either Modern Standard Arabic, French or local dialect -
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MolMarker
Java software to evaluate the results obtained by molecular markers
Journal article to cite: Jahnke, G.; Smidla, J.; Poczai, P. MolMarker: A Simple Tool for DNA Fingerprinting Studies and Polymorphic Information Content Calculation. Diversity 2022, 14, 497. https://doi.org/10.3390/d14060497 Leave a review, please! Your opinion matters! :-) MolMarker is user-friendly software to help evaluate the research results obtained by molecular markers. -
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Matrix Product State (MPS) Simulations
Numerical routines for variational matrix product state simulations.
...We offer various time evolution methods with an emphasis on the support of long-range interactions through the matrix product state formalism. For more algorithms, see the list of features below. Please cite "M. L. Wall and L. D. Carr, New J. Phys. 14, 125015 (2012)" and "D. Jaschke, M. L. Wall, and L. D. Carr, Computer Physics Communications 225, 59–91 (2018)" if your publication involves OSMPS. -
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J-Circos
J-Circos: An Interactive Circos plotter
J-Circos is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. j.an@qut.edu.au please cite An J, Lai J, Sajjanhar A, Batra J, Wang C, et al. J-Circos: an interactive Circos plotter. Bioinformatics. 2015;31:1463–5 -
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PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative...
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Version2. to cite this collection: DOI: http://dx.doi.org/10.12785/ijcds/100161 title={A Combined Method of Naïve-Bayes and Pooling Strategy for Building Test Collection for Arabic/English Information Retrieval}, author={Mazari, Ahmed Cherif and Djeffal, Abdelhamid}, journal={International Journal of Computing and Digital Systems}, volume={10}, year={2021}, publisher={University of Bahrain} }
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Hysteresis
Preisach type hysteresis models implemented in Matlab.
...The derived expressions are included in static and dynamic hysteresis models, which are fast enough to be incorporated in electromagnetic software. If you find the codes usefull, please cite the following papers: [1] Zs. Szabó, J. Füzi, "Implementation and Identification of Preisach type Hysteresis Models with Everett Function in Closed Form", Journal of Magnetism and Magnetic Materials, vol. 406, 15 pp. 251–258, 2016. [2] Zs. Szabó, “Preisach Functions Leading to Closed Form Permeability“, Physica B, vol. 372, pp. 61-67, 2006... -
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U-Net Fusion RFI
U-Net for RFI Detection based on @jakeret's implementation
...You can find this code at https://gitlab.com/aroffringa/aoflagger. This project will use the aoflagger program within the code, so you may need to ensure that any environment variables are set for aoflagger before use. cite: https://sourceforge.net/p/u-net-fusion-rfi/wiki/cite/ -
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scDAPA
Detection and visualization of dynamic alternative polyadenylation
... [2] scDAPA Q&A For Q&A, please visit the Blog page of this website. [3] scDAPA bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite scDAPA? Ye C, Zhou Q, Wu X, Yu C, Saban D.R, Li Q.Q (2020) scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics, 36(4): 1262–1264. https://doi.org/10.1093/bioinformatics/btz701 -
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DEPRECATED - KVFinder
Cavity Detection PyMOL plugin
...[parKVFinder] A Linux/macOS version is available in this GitHub repository, https://github.com/LBC-LNBio/parKVFinder, while a Windows version is in this GitHub repository, https://github.com/LBC-LNBio/parKVFinder-win. Please read and cite the original paper ParKVFinder: A thread-level parallel approach in biomolecular cavity detection (10.1016/j.softx.2020.100606). [pyKVFinder] pyKVFinder is available in this Python Package Index (PyPI) repository, https://pypi.org/project/pyKVFinder and this GitHub repository, https://github.com/LBC-LNBio/pyKVFinder. Please read and cite the original paper pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science (10.1186/s12859-021-04519-4).