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  1. 3121
    “…CONCLUSIONS: The evaluation of the computed results, both through experts’ visual assessments and through the comparison of the computed indexes with those of experts, proved that the prototype is promising, so that experts believe in its potential as a tool to be exploited in the clinical practice as a valid aid for clinicians estimating the ki67-index. The MATLAB source code is open source for research purposes.…”
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    Online Artículo Texto
    ki67 nuclei detection and ki67-index estimation: a novel automatic approach based on human vision modeling
  2. 3122
    “…CONCLUSION: VariFAST can assist researchers efficiently and conveniently to filter the false positive variants, including both germline and somatic ones, in NGS data analysis. The VariFAST source code and the pipeline integrating with GATK Best Practices are available at https://github.com/bioxsjtu/VariFAST.…”
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    VariFAST: a variant filter by automated scoring based on tagged-signatures
  3. 3123
    “…CONCLUSION: Falco is a significantly updated open source big data processing framework that enables scalable and accelerated alignment and assembly of full-length scRNA-seq data on the cloud. The source code can be found at https://github.com/VCCRI/Falco.…”
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    Online Artículo Texto
    Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco
  4. 3124
    por Giorgi, John M, Bader, Gary D
    Publicado 2020
    “…AVAILABILITY AND IMPLEMENTATION: Source code for our biomedical IE tool is available at https://github.com/BaderLab/saber. …”
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    Online Artículo Texto
    Towards reliable named entity recognition in the biomedical domain
  5. 3125
    “…A standalone version of DeepMito is available on DockerHub at https://hub.docker.com/r/bolognabiocomp/deepmito. DeepMito source code is available on GitHub at https://github.com/BolognaBiocomp/deepmito SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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    DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
  6. 3126
    “…Moreover, SAMPN can generate chemically visible and interpretable results, which can help researchers discover new pharmaceuticals and materials. The source code of the SAMPN prediction pipeline is freely available at Github (https://github.com/tbwxmu/SAMPN).…”
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    A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility
  7. 3127
    “…AVAILABILITY AND IMPLEMENTATION: Crossmapper is a command line tool implemented in Python 3.6 and available as a conda package, allowing effortless installation. The source code, detailed information and a step-by-step tutorial is available at our GitHub page https://github.com/Gabaldonlab/crossmapper. …”
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    CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
  8. 3128
    “…CONCLUSIONS: The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.…”
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    GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
  9. 3129
    “…SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing.…”
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    SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
  10. 3130
    “…LIRA was developed to improve the efficiency of histopathology analysis for mouse tuberculosis infection models, this approach has also broader applications to other disease models and tissues. The full source code and documentation is available from https://Github.com/TB-imaging/LIRA.…”
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    Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks
  11. 3131
    “…Our simulation model is capable of addressing additional questions beyond the scope of this article, and we open the simulation software, program manual and source code for free public use.…”
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    Evolution of switchable aposematism: insights from individual-based simulations
  12. 3132
    “…Network data files are at: https://github.com/SuLab/ngly1-graph and source code at: https://github.com/SuLab/bioknowledge-reviewer. …”
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    Structured reviews for data and knowledge-driven research
  13. 3133
    “…It is implemented using portable Docker containers and can easily be deployed locally or on a cloud infrastructure. The source code for building the service is available under an open-source license on GitHub, with a functional image on Docker Hub and can be used by anyone free of charge.…”
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    An open-source GIS-enabled lookup service for Nagoya Protocol party information
  14. 3134
    “…We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. The source code and documentation of SIM are freely available at github.com/desiro/silentMutations.…”
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    SilentMutations (SIM): A tool for analyzing long-range RNA–RNA interactions in viral genomes and structured RNAs
  15. 3135
    por Peng, He
    Publicado 2020
    “…CFSP is implemented in C++ and shell script; the source code and related data are available at https://github.com/HePeng2016/CFSP.…”
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    CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification
  16. 3136
    “…Needlestack, along with its source code is freely available on the GitHub platform: https://github.com/IARCbioinfo/needlestack.…”
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    Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data
  17. 3137
    “…It took 3 h for an experienced researcher for manual analysis. Source code is freely available for download at https://github.com/kablag/AScall. …”
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    AScall – Automatic Allele-Specific qPCR Analysis
  18. 3138
    “…AVAILABILITY AND IMPLEMENTATION: The source code for identifying and quantifying isomiRs and performing miRNA differential expression analysis is available at https://github.com/amanzju/MDEHT. …”
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    MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies
  19. 3139
    “…AVAILABILITY AND IMPLEMENTATION: Documentation, source code and docker containers are available for running PSORTm locally at https://www.psort.org/psortm/ (freely available, open-source software under GNU General Public License Version 3). …”
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    PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data
  20. 3140
    “…ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. …”
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    ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
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