Search Results for "cite"
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Showing 261 open source projects for "cite"
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Zotero
Tool to help you collect, organize, annotate, cite, and share research
Zotero is a powerful, free, open-source research management application designed to help students, academics, and professionals collect, organize, annotate, cite, and share research sources and materials for papers, projects, or books. It can save web pages, PDFs, books, articles, and more with metadata, automatically extract bibliographic information, and organize items into collections and tag systems, while supporting notes and annotations directly alongside references. Zotero’s interface integrates with word processors like Microsoft Word and LibreOffice to generate formatted citations and bibliographies in many styles, and it can sync libraries across devices or share them with collaborators. ... -
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BQSKit
Berkeley Quantum Synthesis Toolkit
The Berkeley Quantum Synthesis Toolkit (BQSKit) [bis • kit] is a powerful and portable quantum compiler framework. It can be used with ease to compile quantum programs to efficient physical circuits for any QPU. A standard workflow utilizing BQSKit consists of loading a program into the framework, modeling the target QPU, compiling the program, and exporting the resulting circuit. -
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adstex
Automated generation of NASA ADS bibtex entries directly from citation
adstex automatically identifies all citation keys (e.g., identifiers, author+year) in your TeX source files and uses NASA's Astrophysics Data System (ADS) to generate corresponding bibtex entries. Write your papers without worrying about the bibtex entries. Simply put down arXiv IDs, ADS bibcodes, DOIs, or first author & year citation keys in your \cite commands, and then use adstex to automatically generate the bibtex file for you. -
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Zettlr
A Markdown Editor for the 21st century
...In other words: No matter where you come from — all Zettelkästen are beautiful and supported by Zettlr. Out of the box. Zettlr integrates well with reference managers such as Zotero, JabRef, or Juris-M. Simply load your library into Zettlr, and begin to cite. Zettlr strictly adheres to established standards and does not reinvent the wheel. -
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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Krylov.jl
A Julia Basket of Hand-Picked Krylov Methods
If you use Krylov.jl in your work, please cite it using the metadata given in CITATION.cff. -
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AndroidTV-x86_64
https://androidtv-x86-64.sourceforge.io
...Android/Google TV x86_64 (also known as ATV/GTV x86_64), this is an entertainment-oriented product, providing simplified operations suitable for all ages. 3. The project is maintained by MRD_Team and individual products are shared here. Note: - Visit our Blog for all the Information and Guide. - Please cite sources if you share on any social media platforms. -
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MixONat
13C-NMR based dereplication software.
MixONat allows the dereplication of natural products mixtures using 13C-NMR and DEPT data. Cite as: Bruguière, Antoine, Derbré, Séverine & Richomme, Pascal. (2020). MixONat (1.0.1) [Software]. SourceForge. https://sourceforge.net/projects/mixonat/ -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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...It can construct linkage maps on very large number of markers and individuals on single or multiple families. Especially, it supports whole genome sequencing data even with low sequencing depth. If you use Lep-MAP3, please cite P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494. Please note Lep-Anchor for anchoring genomes with Lep-MAP3 linkage maps http://sourceforge.net/projects/lep-anchor
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Rom Game Consoles
A collection of games compiled for console emulators.
...This is an add-on for the AndroidTV-x86_64 Entertainment project with a customized Lemuroid emulator to provide the best compatibility. 3. If you don't like our projects, please skip them. Note: - Visit our Blog for all the Information. - Please cite sources if you share on any social media platforms. -
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MatCont
Numerical Bifurcation Analysis Toolbox in Matlab
...Kuznetsov (Utrecht,NL) and Hil G.E. Meijer (UT, Enschede, NL). Matcont for ODEs and MatcontM for Maps Publishing a paper using our software? That's great. Please do us a favour and cite: New features of the software MatCont for bifurcation analysis of dynamical systems. A. Dhooge, and W. Govaerts, Yu.A. Kuznetsov, H.G.E. Meijer and B. Sautois, MCMDS 2008, Vol. 14, No. 2, pp 147-175 In case you're stuck, use the forum, but to get a good answer provide: 1. What command do you give when this appears? Provide the exact steps. ... -
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OCTAVA is designed for quantitative characterization of microvascular archetecture based on OCTA images OCTAVA is available free for use under an MIT licence. If you use this software in your research, please cite the following papers: Untracht, G.R., Durkee, M.S., Zhao, M. et al. Towards standardising retinal OCT angiography image analysis with open-source toolbox OCTAVA. Sci Rep 14, 5979 (2024). https://doi.org/10.1038/s41598-024-53501-6 Untracht GR, Matos RS, Dikaios N, Bapir M, Durrani AK, Butsabong T, et al. (2021) OCTAVA: An open-source toolbox for quantitative analysis of optical coherence tomography angiography images. ...
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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The proper way to cite TRAUPIXE are: 1- L. Pichon, Q. Lemasson, D. Bachiller-Perea, C. Pacheco, Advances in dynamic and batch processing of PIXE spectra, Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 565 (2025) 165734. https://doi.org/10.1016/j.nimb.2025.165734. 2-L. Pichon, T. Calligaro, Q. Lemasson, B. Moignard, C. Pacheco, Programs for visualization, handling and quantification of PIXE maps at the AGLAE facility, Nucl.
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AnaSP
AnaSP, a MATLAB software suite to ANAlyse SPheroids' features
...AnaSP is distributed as an open source software tool, and its modular architecture and graphical user interface make it attractive also for non-Computer Scientist people, and suitable for both high content screenings and occasional spheroid-based experiments. Please, when using AnaSP, cite: "F. Piccinini, AnaSP: a software suite for automatic image analysis of multicellular spheroids. Computer Methods and Programs in Biomedicine, 119(1):43-52, 2015." Requirements: MATLAB R2022a or later versions. -
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...This project was inspired on the Radiomics, and provides a GUI with convenient process. FAE was initially developed by East China Normal University and Siemens Healthineers Ltd. If FAE could help in your project, We appreciate that you could cite this work: FeAture Explorer (FAE): A tool for developing and comparing radiomics models. PLoS One. 2020. DOI: https://doi.org/10.1371/journal.pone.0237587 * The released Windows64 version depends on VC_redist.x64 and OpenSSL * The Video: https://www.bilibili.com/video/BV1J14y1i73p Since the limited by the filesize, the new release could be found in https://pan.baidu.com/s/1xI0ArW_V-_36uIqxIuaNfA?...
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Artifact3-D
Artifact3-D: 3D Analysis and Documentation of Archaeological Artifacts
...Functions are also available for the neat documentation of artifacts. Individual artifacts can be imported, analyzed and their documentation exported, or entire assemblages can be automatically analyzed. Please cite: Grosman L, et al. (2022) Artifact3-D: New software for accurate, objective and efficient 3D analysis and documentation of archaeological artifacts. PLoS ONE 17(6): e0268401. https://doi.org/10.1371/journal.pone.0268401 To install, download "Artifact3-D Installation.zip" available in the Files tab, or click Download (green button) in the Summary tab. ... -
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ToxTrac
Free Animal Tracking Software
...It is robust; very fast; and can handle one or several animals in one or several environments. The program provides useful statistics as output. ToxTrac can be used for fish, insects, rodents, etc. If used, please cite: Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., Andersson, P. L. and Andersson, M. (2018). ToxTrac: a fast and robust software for tracking organisms. Methods in Ecology and Evolution. 9(3):460–464 Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., and Andersson, M. (2017). ToxId: an algorithm to track the identity of multiple animals. ... -
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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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GRAMPC
A gradient-based augmented Lagrangian framework for embedded NMPC
...More details about the algorithm and its performance can be found in the corresponding article published in Optimization and Engeneering. The article is available online under open access at: https://doi.org/10.1007/s11081-018-9417-2. Please cite the paper when you are using results obtained with GRAMPC. -
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luscus
molecular editor and viewer
...The program is developed as a graphical interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z -
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Eventer
Rapid, unbiased, reproducible analysis of synaptic events
...The software is coded in MATLAB, but has been compiled as standalone applications for Windows, Mac and Linux. Please visit the official Eventer website for more info https://eventerneuro.netlify.app/ While the paper is in preparation, please cite as; Winchester, G., Liu, S., Steele, O.G., Aziz, W. and Penn, A.C. (2020) Eventer. Software for the detection of spontaneous synaptic events measured by electrophysiology or imaging. http://doi.org/10.5281/zenodo.3991676 -
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Docking-Affinity-Plotter
Docking Affinity Plotter: Visualize and analyze binding affinity data.
... ✅ Binding affinity distribution ✅ Density plot of binding affinity ✅ Box plot of binding affinity ✅ RMSD distribution (ub & lb) ✅ 3D scatter plot: Binding affinity vs RMSD ✅ Scatter plots: Affinity vs RMSD ub/lb ✅ Pairwise relationships among affinity and RMSD values ✅ Top 10 ligands by minimum binding affinity ✅ Top 3 recommended ligands ✅ Statistical analysis Citation If you use Docking Affinity Plotter in your research, please cite it as: Md. Ismiel Hossen, A. (2026). Docking Affinity Plotter: Visualize and Analyze Binding Affinity Data (v1.0). Zenodo. https://doi.org/10.5281/zenodo.18340175 -
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C-BerryTrans
Calculation of Berry-curvature-driven AHC or ANC using WIEN2k
...To ensure efficiency, the code parallelizes Berry curvature evaluation over k-points using OpenMP and stores band-resolved data in binary format, enabling rapid post-processing of AHC and ANC across a wide range of chemical potentials and temperatures in a single run. Please cite the paper mentioned below while using the C-BerryTrans code for your research: V. Pandey and S.K. Pandey, https://arxiv.org/abs/2509.24071.
