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  1. 2201
    “…AVAILABILITY AND IMPLEMENTATION: PHi-C2 as the phic Python package is freely available under the GPL license and can be installed from the Python package index. The source code is available from GitHub at https://github.com/soyashinkai/PHi-C2. …”
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    PHi-C2: interpreting Hi-C data as the dynamic 3D genome state
  2. 2202
    “…Two datasets are analyzed in this manuscript: one composed of 204 urine samples from neonates and infants (≤3 months old) attended in the emergency department with suspected UTI; and the second dataset including 1174 urines samples from an elderly population attended at the primary care level. The source code is available on GitHub (https://github.com/GuillermoMG-HUVR/Microbiology-applications/tree/FlowUTI/FlowUTI). …”
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    FlowUTI: An interactive web-application for optimizing the use of flow cytometry as a screening tool in urinary tract infections
  3. 2203
    “…AVAILABILITY AND IMPLEMENTATION: The source code of App-SpaM is freely available on Github at https://github.com/matthiasblanke/App-SpaM together with detailed instructions for installation and settings. …”
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    App-SpaM: phylogenetic placement of short reads without sequence alignment
  4. 2204
    “…AVAILABILITY AND IMPLEMENTATION: The source code for the implementation of this genomic style method, along with the dataset for the performance evaluation, is available from https://github.com/friendflower94/binning-style. …”
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    Genomic style: yet another deep-learning approach to characterize bacterial genome sequences
  5. 2205
    “…AVAILABILITY AND IMPLEMENTATION: The source code and data of this study are available at https://github.com/BiOmicsLab/TransImbAMP. …”
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    Online Artículo Texto
    Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities
  6. 2206
    por Cai, Dehan, Shang, Jiayu, Sun, Yanni
    Publicado 2022
    “…AVAILABILITY AND IMPLEMENTATION: The source code and the documentation of HaploDMF are available at https://github.com/dhcai21/HaploDMF. …”
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    HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization
  7. 2207
    por Wacquet, Guillaume, Lefebvre, Alain
    Publicado 2022
    “…It is implemented in R and calls Python scripts for image classification step (using reticulate and tensorflow libraries). The source code, instruction manual and examples can be found at https://github.com/IFREMER-LERBL/EcoTransLearn. …”
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    EcoTransLearn: an R-package to easily use transfer learning for ecological studies—a plankton case study
  8. 2208
    “…AVAILABILITY AND IMPLEMENTATION: The source code of Galaxy-methyl is available at https://github.com/fengyilin118/.…”
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    GPU-accelerated and pipelined methylation calling
  9. 2209
    “…Furthermore, analyzing the effect of the improved sections provided insight into handling pooled single-cell data in the future. Our source code of the devised software is available at GitHub: https://github.com/kaistcbfg/scAVENGERS.…”
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    scAVENGERS: a genotype-based deconvolution of individuals in multiplexed single-cell ATAC-seq data without reference genotypes
  10. 2210
    “…AVAILABILITY AND IMPLEMENTATION: The CSREP source code and generated data are available at http://github.com/ernstlab/csrep. …”
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    A framework for group-wise summarization and comparison of chromatin state annotations
  11. 2211
    “…AVAILABILITY AND IMPLEMENTATION: A user-friendly webserver of sAMPpred-GAT can be accessed at http://bliulab.net/sAMPpred-GAT and the source code is available at https://github.com/HongWuL/sAMPpred-GAT/. …”
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    sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure
  12. 2212
    por Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary
    Publicado 2022
    “…AVAILABILITY AND IMPLEMENTATION: The new GSEApy with Rust extension is deposited in PyPI: https://pypi.org/project/gseapy/. The GSEApy source code is freely available at https://github.com/zqfang/GSEApy. …”
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    GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
  13. 2213
    “…AVAILABILITY AND IMPLEMENTATION: Source code and details for the implementation of SEGCOND is available at https://github.com/AntonisK95/SEGCOND SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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    SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data
  14. 2214
    “…AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/Zhangxf-ccnu/EnDecon. …”
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    EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning
  15. 2215
    “…AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/nabiafshan/DetectingMisannotatedLncRNAs. …”
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    Discovering misannotated lncRNAs using deep learning training dynamics
  16. 2216
    “…The parametric approach was developed as a Python package (cmangoes), the source code and documentation of which can be found at https://github.com/ghattab/cmangoes and https://doi.org/10.5281/zenodo.7483771.…”
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    A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
  17. 2217
    por Viesná, Е., Fishman, V.
    Publicado 2022
    “…The FastContext package is available at the Python Package Index (https://pypi.org/project/FastContext), the source code is available at GitHub (https://github.com/regnveig/FastContext).…”
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    FastContext: A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data
  18. 2218
    “…CONCLUSIONS: xAtlas is a fast, lightweight, and accurate SNV and small indel calling method. Source code for xAtlas is available under a BSD 3-clause license at https://github.com/jfarek/xatlas.…”
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    xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments
  19. 2219
    “…DRAGON is available as open-source code in Python through the Network Zoo package (netZooPy v0.8; netzoo.github.io).…”
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    DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks
  20. 2220
    por Bertels, Koen
    Publicado 2012
    “…The tool chain takes existing source code and proposes transformations and mappings such that legacy code can easily be ported to a modern, multi-core platform. …”
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    HardwareSoftware Co-design for Heterogeneous Multi-core Platforms: The hArtes Toolchain
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