displayHTS: a R package for displaying data and results from high-throughput screening experiments

By Xiaohua Douglas Zhang, Zhaozhi Zhang. Bioinform., 2013

6,317 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/3f3d4dc314f1ecdb246a6d22a0b51edaa6f82fd6

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In Molecular Biology

Citations in the corpus

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary (2016, methodology): “Assemblies were annotated with PROKKA 1.11 [32] using the Staphylococcus genus database.”
Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum (2023, methodology): “14.5 (Seemann, 2014) with specific parameters ('—metagenome’) then annotated by KOfam and custom HMM profiles within METABOLIC v.4.0 (Zhou et al., 2022) and eggNOG-emapper v.2.1.2 (Cantalapiedra et al., 2021) with default settings.”
Next-Generation Sequencing Technology: Current Trends and Advancements (2023, neutral): “Shotgun Metagenomics Taxonomic classification MetaPhlAn4 [158], Kaiju [159], Kraken [160] Assembly of metagenomic reads metaSPAdes [86], metaIDBA [87] Protein databases for taxonomic classification NCBI non-redundant protein database [83] Gene annotation Prokka [88], MetaGeneMark [89] Databases for ”
Proksee: in-depth characterization and visualization of bacterial genomes (2023, background): “More recently, command-line-dri v en programs such as Prokka ( 7 ), Bakta ( 8 ) and PGAP ( 9 ) have become popular since they allow for the annotation of large numbers of genomes in high-performance computing environments.”
Pharokka: a fast scalable bacteriophage annotation tool (2022, methodology): “Existing tools such as RAST (Aziz et al., 2008; Davis et al., 2020), PHASTER (Arndt et al., 2016) and CPT Galaxy (Ramsey et al., 2020) are web-server based which may be laborious in particular when multiple phage genomes require annotation (Shen and Millard, 2021).”