Bioinformatics

  1. Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

    1. Zhanghan Ni
    2. Troy Osborn
    3. Juntao Zhong
    4. Adrian Gonzalez
    5. Will Puzella
    6. Aya Klos
    7. Bryan Le
    8. Alec Leonetti
    9. Joanne S Boden
    10. Eva E Stueeken
    11. Rika E Anderson

    Reviewed by Arcadia Science

    1 evaluationAppears in 1 listLatest version Latest activity

  2. Direct Comparative Analyses of 10X Genomics Chromium and Smart-Seq2

    1. Xiliang Wang
    2. Yao He
    3. Qiming Zhang
    4. Xianwen Ren
    5. Zemin Zhang

    Reviewed by PREreview

    1 evaluationAppears in 1 listLatest version Latest activity

  3. pyRootHair: Machine learning accelerated software for high-throughput phenotyping of plant root hair traits

    1. Ian Tsang
    2. Lawrence Percival-Alwyn
    3. Stephen Rawsthorne
    4. James Cockram
    5. Fiona Leigh
    6. Jonathan A Atkinson

    Reviewed by GigaScience

    2 evaluationsAppears in 1 listLatest version Latest activity

  4. EMImR: a Shiny application for identifying transcriptomic and epigenomic changes

    1. Hiba Ben Aribi
    2. Careen Naitore
    3. Farah Ayadi
    4. Souheila Guerbouj
    5. Olaitan I. Awe

    • Curated by GigaByte

      Editors Assessment:

      Coded and written up as part of the African Society for Bioinformatics and Computational Biology (ASBCB) Omicscodeathons, EMImR is a novel Shiny application for transcriptomic and epigenomic change identification and correlation wrapped up using a combination of Bioconductor and CRAN packages. Case studies are on publicly available GEO data corresponding to sequencing data of human blood cell samples of multiple sclerosis patients to demonstrate how the tool works. And a documentation and videos are provided. Peer review and the study highlighting the usefulness of the developed tool for analyzing transcriptomic and epigenomic data.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    2 evaluationsAppears in 2 listsLatest version Latest activity

  5. Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

    1. Simon Holzinger
    2. Leo Schmutterer
    3. Victoria Marie Rothe
    4. Maria Theresia Watzlowik
    5. Uwe Schwartz
    6. Gernot Längst

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity

  6. MAVISp : A modular structure‐based framework for protein variant effects

    1. Matteo Arnaudi
    2. Mattia Utichi
    3. Kristine Degn
    4. Matteo Tiberti
    5. Ludovica Beltrame
    6. Karolina Krzesińska
    7. Pablo Sánchez‐Izquierdo Besora
    8. Eleni Kiachaki
    9. Simone Scrima
    10. Laura Bauer
    11. Katrine Meldgård
    12. Anna Melidi
    13. Lorenzo Favaro
    14. Anu Oswal
    15. Guglielmo Tedeschi
    16. Terézia Dorčaková
    17. Alberte Heering Estad
    18. Joachim Breitenstein
    19. Jordan Safer
    20. Paraskevi Saridaki
    21. Valentina Sora
    22. Francesca Maselli
    23. Philipp Becker
    24. Jérémy Vinhas
    25. Alberto Pettenella
    26. Matteo Lambrughi
    27. Claudia Cava
    28. Anna Rohlin
    29. Mef Nilbert
    30. Sumaiya Iqbal
    31. Peter Wad Sackett
    32. Burcu Aykac Fas
    33. Elena Papaleo

    Reviewed by Review Commons

    8 evaluationsAppears in 2 listsLatest version Latest activity

  8. ParTIpy: A Scalable Framework for Archetypal Analysis and Pareto Task Inference

    1. Philipp S. L. Schäfer
    2. Leoni Zimmermann
    3. Paul L. Burmedi
    4. Avia Walfisch
    5. Noa Goldenberg
    6. Shira Yonassi
    7. Einat Shaer Tamar
    8. Miri Adler
    9. Jovan Tanevski
    10. Ricardo O. Ramirez Flores
    11. Julio Saez-Rodriguez

    Reviewed by Review Commons

    3 evaluationsAppears in 1 listLatest version Latest activity

  9. Human single-cell atlas analysis reveals heterogeneous endothelial signaling

    1. Zimo Zhu
    2. Rongbin Zheng
    3. Yang Yu
    4. Lili Zhang
    5. Kaifu Chen

    Reviewed by preLights

    1 evaluationAppears in 1 listLatest version Latest activity
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