Collate usage in papers/repos to glean what we can do better

[sckott]

• article: https://peerj.com/articles/4662/ code: https://dfzljdn9uc3pi.cloudfront.net/2018/4662/1/RADseq_microbiome_code.R
  • used: classification
• article: https://www.pnas.org/content/115/51/13027/ code: https://github.com/AnahiEspindola/PelletierEtAlPNAS/blob/9b1f363dba3baddd31c084738d6bff18534edda8/SpatialMorpho/PrepareDatasets.R
  • used: classification
• article: https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.12820 code: https://figshare.com/articles/Data_and_code_to_reproduce_Dallas_and_Hastings_2018_Habitat_suitability_estimated_by_niche_models_is_largely_unrelated_to_species_abundance_/6026777
  • don't see any taxize code here
• article: https://academic.oup.com/nar/article/47/W1/W542/5498618 code: https://github.com/UCSC-LoweLab/tRNAviz-data/blob/dfe5bb166b9bc9b64ae44b64705d407bff209ea4/get-taxonomy.R
  • used: classification
• article: https://pubs.acs.org/doi/10.1021/acs.est.9b00893 (code in SI, in file scripts/heatmap.R in the zip file)
  • used: classification, class2tree
• article: https://academic.oup.com/gigascience/article/8/4/giz029/5450733#133648256 code: https://github.com/alexcrampton-platt/screenforbio-mbc/blob/master/get_taxonomy_mismatches.R
  • used: classification
• article: https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.4809 code: https://github.com/tobiasgf/Bioinformatic-tools/blob/b99d0a5cacb7b480a614908a38e6de6a40281caf/Eva_Sigsgaard_2018/Tobias_taxonomy_v3_181030.r
  • used: classification
• article: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5516-5 code: no code, but mentioned in text
  • used: classification