Terrier Experimental Data

<p dir="ltr">This repository contains the data for the application of <a href="https://github.com/rbturnbull/terrier" rel="noreferrer" target="_blank">Terrier</a> to experimental data. See also: <a href="https://github.com/rbturnbull/terrier-experimental-data" target="_blank">https://github.com/rbturnbull/terrier-experimental-data</a></p><p dir="ltr">There are 8 libraries of transposable elements (TEs) from flatworms. See the following directories:</p><ul><li>flatworms/Clonorchis_sinensis</li><li>flatworms/Dicrocoelium_dendriticum</li><li>flatworms/Fasciola_hepatica</li><li>flatworms/Fasciolopsis_buski</li><li>flatworms/Schistosoma_haematobium</li><li>flatworms/Schistosoma_japonicum</li><li>flatworms/Schistosoma_mansoni</li><li>flatworms/Trichobilharzia_regenti</li></ul><p dir="ltr">Schistosoma mansoni also has a FASTA file with 21 TEs annotated in the NCBI database.</p><p dir="ltr">There are 51 libraries of TEs from amphibians:</p><ul><li>amphibians/Allobates_femoralis</li><li>amphibians/Ambystoma_mexicanum</li><li>amphibians/Bombina_bombina</li><li>amphibians/Bombina_variegata</li><li>amphibians/Bufo_bufo</li><li>amphibians/Bufo_gargarizans</li><li>amphibians/Dendropsophus_ebraccatus</li><li>amphibians/Discoglossus_pictus</li><li>amphibians/Eleutherodactylus_coqui</li><li>amphibians/Engystomops_pustulosus</li><li>amphibians/Gastrophryne_carolinensis</li><li>amphibians/Geotrypetes_seraphini</li><li>amphibians/Glandirana_rugosa</li><li>amphibians/Hyalinobatrachium_fleischmanni</li><li>amphibians/Hyla_sarda</li><li>amphibians/Hymenochirus_boettgeri</li><li>amphibians/Leptobrachium_ailaonicum</li><li>amphibians/Leptobrachium_leishanense</li><li>amphibians/Leptodactylus_fallax</li><li>amphibians/Limnodynastes_dumerilii</li><li>amphibians/Lithobates_catesbeianus</li><li>amphibians/Lithobates_sylvaticus</li><li>amphibians/Mantella_aurantiaca</li><li>amphibians/Microcaecilia_unicolor</li><li>amphibians/Nanorana_parkeri</li><li>amphibians/Oophaga_pumilio</li><li>amphibians/Oophaga_sylvatica</li><li>amphibians/Pelobates_cultripes</li><li>amphibians/Phrynoglossus_myanhessei</li><li>amphibians/Phyllomedusa_bahiana</li><li>amphibians/Pipa_carvalhoi</li><li>amphibians/Pipa_parva</li><li>amphibians/Platyplectrum_ornatum</li><li>amphibians/Pleurodeles_waltl</li><li>amphibians/Pseudophryne_corroboree</li><li>amphibians/Pyxicephalus_adspersus</li><li>amphibians/Rana_kukunoris</li><li>amphibians/Rana_muscosa</li><li>amphibians/Rana_temporaria</li><li>amphibians/Ranitomeya_imitator</li><li>amphibians/Rhinatrema_bivittatum</li><li>amphibians/Rhinella_marina</li><li>amphibians/Scaphiopus_couchii</li><li>amphibians/Scaphiopus_holbrookii</li><li>amphibians/Spea_bombifrons</li><li>amphibians/Spea_hammondii</li><li>amphibians/Spea_multiplicata</li><li>amphibians/Staurois_parvus</li><li>amphibians/Xenopus_borealis</li><li>amphibians/Xenopus_laevis</li><li>amphibians/Xenopus_tropicalis</li></ul><p dir="ltr">Most amphibian repeat libraries were generated using RepeatModeler version 2.0.4 (excluding the LTR pipeline extensions by Jullien M. Flynn). Ambistoma mexicanum was generated using RepeatModeler version 2.0.5.</p><p dir="ltr">Each directory contains:</p><ul><li>a FASTA file with extension .fa with the library of TE sequences.</li><li>a CSV file with the predictions from Terrier</li><li>a plot comparing the Terrier predictions with the original annotations (XXXXXXX-comparison.png)</li><li>a plot with the confusion matrix base on the original annotations (XXXXXXX-confusion.png)</li></ul><p dir="ltr">A summary CSV of the results is found in `summary.csv`.</p><p dir="ltr">To reproduce the plot in the paper from the summary, run `plot-summary.py`. This script requires the same virtual environment as Terrier.</p><p dir="ltr">For more instructions, see: <a href="https://github.com/rbturnbull/terrier-experimental-data" target="_blank">https://github.com/rbturnbull/terrier-experimental-data</a></p><h3>Credits</h3><p>Terrier was developed by:</p><ul><li><a href="https://robturnbull.com" rel="noreferrer" target="_blank">Robert Turnbull</a></li><li><a href="https://findanexpert.unimelb.edu.au/profile/249669-neil-young" rel="noreferrer" target="_blank">Neil D. Young</a></li><li><a href="https://findanexpert.unimelb.edu.au/profile/428364-edoardo-tescari" rel="noreferrer" target="_blank">Edoardo Tescari</a></li><li><a href="https://findanexpert.unimelb.edu.au/profile/451921-lee-skerratt" rel="noreferrer" target="_blank">Lee F. Skerratt</a></li><li><a href="https://findanexpert.unimelb.edu.au/profile/775927-tiffany-kosch" rel="noreferrer" target="_blank">Tiffany A. Kosch</a></li></ul><p dir="ltr">If you use this dataset, cite the Terrier paper. See more information at: <a href="https://github.com/rbturnbull/terrier" rel="noreferrer" target="_blank">https://github.com/rbturnbull/terrier</a></p>