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  1. 3681
    “…Its approach is suitable for the simultaneous estimation of protein-coding, long non-coding and small non-coding transcript concentration, in both precursor and processed forms. Both source code and compiled software are available at https://github.com/hitaandrea/MGcount. …”
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    MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts
  2. 3682
    “…To facilitate ML model development for AMR prediction, we packaged every step into an automated pipeline and shared the source code at https://github.com/KuangXY3/MTB-AMR-classification-CNN.…”
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    Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN
  3. 3683
    “…The main contribution of CSMDDI contains the development of a generalized framework to predict the single-type and multi-type of DDIs in the cold start scenario, as well as the implementations of several embedding models for both single-type and multi-type of DDIs. The dataset and source code can be accessed at https://github.com/itsosy/csmddi. …”
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    Predict multi-type drug–drug interactions in cold start scenario
  4. 3684
    “…NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis. …”
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    NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects
  5. 3685
    “…GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). …”
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    GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
  6. 3686
    “…SAPFIR is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/sapfir/, a website implemented in Python, with all major browsers supported. The source code is available at https://github.com/DelongZHOU/SAPFIR. …”
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    SAPFIR: A webserver for the identification of alternative protein features
  7. 3687
    por Wickramarachchi, Anuradha, Lin, Yu
    Publicado 2022
    “…Binning also helps to reduce the resources required for assembly. Source code for LRBinner is freely available at https://github.com/anuradhawick/LRBinner. …”
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    Binning long reads in metagenomics datasets using composition and coverage information
  8. 3688
    “…Finally, the open-source and modularized nature of Cell-ACDC will enable simple and fast integration of new deep learning-based and traditional methods for cell segmentation, tracking, and downstream image analysis. Source code: https://github.com/SchmollerLab/Cell_ACDC SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-022-01372-6.…”
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    Segmentation, tracking and cell cycle analysis of live-cell imaging data with Cell-ACDC
  9. 3689
    “…CONCLUSIONS: PDGPCS can more accurately identify the personalized driver genes and takes a step further toward personalized medicine and treatment. The source code of PDGPCS can be freely downloaded from https://github.com/NWPU-903PR/PDGPCS. …”
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    Prioritization of cancer driver gene with prize-collecting steiner tree by introducing an edge weighted strategy in the personalized gene interaction network
  10. 3690
    “…The software tool has been made available on the Python package index and the source code can be found on GitHub here: https://github.com/cnickh/wgdtree. …”
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    WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events
  11. 3691
    “…Since we further provide the plugin as open‐source code, we expect EVAnalyzer to not only be a resource of immediate impact, but an open innovation platform for the EV and nanoparticle research communities.…”
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    EVAnalyzer: High content imaging for rigorous characterisation of single extracellular vesicles using standard laboratory equipment and a new open‐source ImageJ/Fiji plugin
  12. 3692
    “…CONCLUSION: Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.…”
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    eSMC: a statistical model to infer admixture events from individual genomics data
  13. 3693
    “…MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub (https://github.com/zmahnoor14/MAW). …”
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    MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry
  14. 3694
    “…In summary, functional similarities, dimension reduction and clustering methods, coupled with interactive visualization and control over analysis allows biologists to explore and analyze their datasets without requiring expert knowledge on these methods. The source code of proposed application is available at https://github.com/Muh-Asif/DGH-GO SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05290-4.…”
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    DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology
  15. 3695
    “…These classifications were validated against self-reported data from the Health in Central Denmark survey – overall and stratified by age at onset of diabetes. The source-code of both classifiers was made available in the open-source R package osdc. …”
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    Validation of Register-Based Diabetes Classifiers in Danish Data
  16. 3696
    por Louw, Candice
    Publicado 2023
    “…Despite the open nature of such OSS solutions’ source code, software solutions (both OSS and non-OSS) are only as transparent as the live or production environment where their processed data is hosted or stored. …”
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    Digital Public Health Solutions in Response to the COVID-19 Pandemic: Comparative Analysis of Contact Tracing Solutions Deployed in Japan and Germany
  17. 3697
    “…ForestSubtype outperforms the other two methods in terms of the distribution of clusters, internal and external metric results. The open-source code is available at https://github.com/lffyd/ForestSubtype. …”
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    ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest
  18. 3698
    “…CONCLUSIONS: ECL 3.0 source code is available at https://github.com/yuweichuan/ECL-PF.git. …”
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    ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis
  19. 3699
    “…Our proposed model and source code were made publicly available.…”
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    Improving MR image quality with a multi-task model, using convolutional losses
  20. 3700
    “…Measures of correspondence of shared semantic domain of 0 (perfect match), 1 (fully inclusive match), 2 (partial match), 4 (transformation required) or 4* (not present in ORCHESTRA) as compared to the target code system, ORCHESTRA study variables, were assigned to each of the elements in the ISARIC FUP case report form (CRF) which was considered the source code system. Of the ISARIC FUP CRF’s variables, around 34% were found to show an exact match with corresponding variables in ORCHESTRA studies and about 33% showed a non-inclusive overlap. …”
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    ISO/TS 21564:2019- based Evaluation of a Semantic Map between Variables in the ISARIC Freestanding Follow Up Survey and ORCHESTRA Studies
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