ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics

  • 1.

    Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66.

    Article 

    Google Scholar
     

  • 2.

    Minio A, Lin J, Gaut BS, Cantu D. How single molecule real-time sequencing and haplotype phasing have enabled reference-grade diploid genome assembly of wine grapes. Front Plant Sci. 2017;8:826.

    Article 

    Google Scholar
     

  • 3.

    R Core Team: R: A language and environment for statistical computing. In: R Foundation for Statistical Computing; 2017.

  • 4.

    Calcino AD, Kenny NJ, Gerdol M: Single individual structural variant detection uncovers widespread hemizygosity in molluscs. bioRxiv 2020:2020.2009.2015.298695.

  • 5.

    Mazumdar P, Chiun OY, Lau S-E, Taheri S, Harikrishna JA: The banana (Musa acuminata) MYB gene family and MaMYB14, MaMYB63 and MaMYB110 expression in response to salinity-stress in cv. Berangan. Plant Biosystems—An International Journal Dealing with all Aspects of Plant Biology 2020:1–15.

  • 6.

    McCartney A, Hilario E, Choi S-S, Guhlin J, Prebble JM, Houliston G, Buckley TR, Chagné D: An exploration of assembly strategies and quality metrics on the accuracy of the Knightia excelsa (rewarewa) genome. bioRxiv 2020:2020.2010.2028.358903.

  • 7.

    Negrini F, O’Grady K, Hyvonen M, Folta KM, Baraldi E. Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry. PLoS ONE. 2020;15(3):e0226448.

    CAS 
    Article 

    Google Scholar
     

  • 8.

    Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, et al. 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nat Methods. 2020;17(8):822–32.

    CAS 
    Article 

    Google Scholar
     

  • 9.

    Tirnaz S, Bayer PE, Inturrisi F, Zhang F, Yang H, Dolatabadian A, Neik TX, Severn-Ellis A, Patel DA, Ibrahim MI, et al. Resistance gene analogs in the brassicaceae: identification, characterization, distribution, and evolution. Plant Physiol. 2020;184(2):909–22.

    CAS 
    Article 

    Google Scholar
     

  • 10.

    Wang C, Chen L, Yang Y, Zhang M, Wong G. Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis. Clin Epigenet. 2019;11(1):24.

    CAS 
    Article 

    Google Scholar
     

  • 11.

    Chidzanga C, Fleury D, Baumann U, Mullan D, Watanabe S, Kalambettu P, Pontre R, Edwards J, Forrest K, Wong D, et al. Development of an australian bread wheat nested association mapping population, a new genetic diversity resource for breeding under dry and hot climates. Int J Mol Sci. 2021;22(9):4348.

    CAS 
    Article 

    Google Scholar
     

  • 12.

    Jain R, Ramaswamy S, Harilal D, Uddin M, Loney T, Nowotny N, Alsuwaidi H, Varghese R, Deesi Z, Alkhajeh A, et al. Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes. Comput Struct Biotechnol J. 2020;19:153–60.

    Article 

    Google Scholar
     

  • 13.

    Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, et al. Ensembl 2020. Nucleic Acids Res. 2020;48(D1):D682–8.

    CAS 
    PubMed 

    Google Scholar
     

  • 14.

    Konate M, Wilkinson MJ, Mayne BT, Pederson SM, Scott ES, Berger B, Rodriguez Lopez CM. Salt stress induces non-CG methylation in coding regions of barley seedlings (Hordeum vulgare). Epigenomes. 2018;2(2):12.

    Article 

    Google Scholar
     

  • 15.

    Gollavilli P, Kanugula A, Pemmasani S, Kotamraju S. A newly identified spliced isoform of metadherin differently regulates the global transcriptomic profile in MCF-7 breast cancer cells. NCBI GEO database.

  • 16.

    Casanova EA, Okoniewski MJ, Cinelli P. Cross-species genome wide expression analysis during pluripotent cell determination in mouse and rat preimplantation embryos. PLoS ONE. 2012;7(10):e47107–e47107.

    CAS 
    Article 

    Google Scholar
     

  • Read more here: Source link