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  1. 881
    “…The server is completely free and requires no registration. The C++ source code is available at: https://github.com/starbeachlab/smoothT.…”
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    SmoothT—a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling
  2. 882
    por Wirth, Joseph S, Bush, Eliot C
    Publicado 2023
    “…In this study, we describe the workflow of PHANTASM and provide several examples of results generated by it. The source code is freely-available on GitHub. In order to facilitate the ease-of-access for researchers, PHANTASM is also available as a Docker image. …”
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    Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
  3. 883
    por Larralde, Martin, Zeller, Georg
    Publicado 2023
    “…Pre-compiled packages are released via PyPI (https://pypi.org/project/pyhmmer/) and Bioconda (https://anaconda.org/bioconda/pyhmmer). The PyHMMER source code is available under the terms of the open-source MIT licence and hosted on GitHub (https://github.com/althonos/pyhmmer); its documentation is available on ReadTheDocs (https://pyhmmer.readthedocs.io).…”
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    PyHMMER: a Python library binding to HMMER for efficient sequence analysis
  4. 884
    “…We also described a new PCR-free modular cloning system for multiplexing gRNA, and used it to knockout three tandemly arrayed genes in another multi-gene cluster with gRNA designed by MINORg. Source code is freely available at https://github.com/rlrq/MINORg.…”
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    Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg
  5. 885
    “…AVAILABILITY: CellProfiler Analyst binaries for Windows and MacOS are freely available for download at https://cellprofileranalyst.org/. Source code is implemented in Python 3 and is available at https://github.com/CellProfiler/CellProfiler-Analyst/. …”
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    CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis
  6. 886
    “…These results provide solid algorithmic foundations for comparing genome graphs and point to the direction of heuristics. The source code to reproduce experimental results is available at https://github.com/Kingsford-Group/gtednewilp/.…”
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    Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants
  7. 887
    “…We evaluate PSNSleep on Sleep-EDF and ISRUC-Sleep and achieve accuracy of 80.0% and 74.4%. The source code is publicly available at https://github.com/arthurxl/PSNSleep.…”
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    PSNSleep: a self-supervised learning method for sleep staging based on Siamese networks with only positive sample pairs
  8. 888
    “…It is distributed under the MIT license, and its source code can be found at https://github.com/ebi-webcomponents/nightingale.…”
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    Nightingale: web components for protein feature visualization
  9. 889
    “…AVAILABILITY AND IMPLEMENTATION: The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.…”
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    UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales
  10. 890
    “…AVAILABILITY AND IMPLEMENTATION: Source code is freely available at https://github.com/sebastian-gregoricchio/snHiC. …”
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    snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis
  11. 891
    por Häntze, Hartmut, Horton, Paul
    Publicado 2023
    “…AVAILABILITY AND IMPLEMENTATION: The source code of our proposed tool MaskedPanGenie is openly available on https://github.com/hhaentze/MaskedPangenie.…”
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    Effects of spaced k-mers on alignment-free genotyping
  12. 892
    “…AVAILABILITY AND IMPLEMENTATION: Plassembler is implemented in Python and is installable as a bioconda package using ‘conda install -c bioconda plassembler’. The source code is available on GitHub at https://github.com/gbouras13/plassembler. …”
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    Plassembler: an automated bacterial plasmid assembly tool
  13. 893
    “…AVAILABILITY AND IMPLEMENTATION: The Python package SEAGAL can be installed using pip: https://pypi.org/project/seagal/. The source code and step-by-step tutorials are available at: https://github.com/linhuawang/SEAGAL.…”
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    Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
  14. 894
    “…AVAILABILITY AND IMPLEMENTATION: The source code, extensive documentation, and tutorials are freely available on GitHub at https://github.com/francescodc87/ipaPy2…”
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    ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0—an improved Bayesian-based method for the annotation of LC–MS/MS untargeted metabolomics data
  15. 895
    “…The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses.…”
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    Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond
  16. 896
    “…AVAILABILITY AND IMPLEMENTATION: The source code repository is publicly available at https://github.com/hsjeon1217/conditional_method.…”
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    Adjusting for gene-specific covariates to improve RNA-seq analysis
  17. 897
    “…AVAILABILITY AND IMPLEMENTATION: The web server of PhaBOX is available via: https://phage.ee.cityu.edu.hk. The source code of PhaBOX is available at: https://github.com/KennthShang/PhaBOX.…”
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    PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data
  18. 898
    “…AVAILABILITY AND IMPLEMENTATION: Gonomics is implemented in the Go programming language. Source code, installation instructions, and documentation are freely available at https://github.com/vertgenlab/gonomics.…”
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    Gonomics: uniting high performance and readability for genomics with Go
  19. 899
    “…AVAILABILITY AND IMPLEMENTATION: The program web server is available at http://iimcb.genesilico.pl/rnamasonry. The source code is available at https://gitlab.com/gchojnowski/rnamasonry.…”
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    RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
  20. 900
    “…AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/yuzhong-deng/graphcpg.git.…”
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    GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs
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