orthomap - example data
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Example data for python package orthomap. Includes OrthoFinder results for all translated coding sequences (CDS) from Ensembl release-105 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: <ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip> <ensembl_105_orthofinder_Orthogroups.zip.tsv> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <ensembl_105_orthofinder_species_list.tsv> Includes NCBI taxonomic tree for Ensembl release-105 species analysed: <ensembl_105_species_tree_ncbi_topology_named.nw> <ensembl_105_species_tree_ncbi_topology_named.pdf> Includes pre-calculated gene age assignments for C. elegans (Sun et al. 2021) and H. vulgaris (Cazet et al. 2022): <Sun2021_Orthomap.tsv> <Cazet2022_Orthomap.tsv> Includes pre-calculated TajimaD, NormalizedPi, FayWu, Fst for C. elegans (Ma et al. 2021): <Ma2021_Fst.tsv> Includes extracted orthomaps for all Eukaryota from eggNOG database version 6.0 (Hernández-Plaza et al. 2022): <eggnog6_eukaryota_orthomaps.tsv.zip> Includes example data from the myTAI R package (Drost et al. 2018) <PhyloExpressionSetExample.h5ad> Includes extracted orthomaps for either HOMFAM or ORTHOFAM groups of plants from PLAZA database version 5.0 (Van Bel et al. 2022): <plaza_v5_dicots_HOMFAM_orthomaps.tsv.zip> <plaza_v5_dicots_ORTHOFAM_orthomaps.tsv.zip> <plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip> <plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip>
本数据集为Python包orthomap的示例数据，涵盖源自Ensembl 105版（仅保留最长转录本）的所有翻译编码序列（Coding Sequence, CDS）以及来自xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的OrthoFinder分析结果，对应文件为<ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip>与<ensembl_105_orthofinder_Orthogroups.zip.tsv>；涵盖一份列明OrthoFinder分析所用物种文件名及其对应NCBI分类学ID的表格，文件为<ensembl_105_orthofinder_species_list.tsv>；涵盖本次分析涉及的Ensembl 105版物种的NCBI分类学树文件，分别为<ensembl_105_species_tree_ncbi_topology_named.nw>与<ensembl_105_species_tree_ncbi_topology_named.pdf>；涵盖针对秀丽隐杆线虫（C. elegans, Sun et al. 2021）与水螅（H. vulgaris, Cazet et al. 2022）的预计算基因年龄赋值数据，对应文件为<Sun2021_Orthomap.tsv>与<Cazet2022_Orthomap.tsv>；涵盖针对秀丽隐杆线虫（Ma et al. 2021）的预计算TajimaD、标准化核苷酸多样性（NormalizedPi）、FayWu统计量以及种群分化指数Fst数据，文件为<Ma2021_Fst.tsv>；涵盖从eggNOG数据库6.0版（Hernández-Plaza et al. 2022）中提取的所有真核生物同源映射表数据，文件为<eggnog6_eukaryota_orthomaps.tsv.zip>；涵盖来自myTAI R包（Drost et al. 2018）的示例数据，文件为<PhyloExpressionSetExample.h5ad>；涵盖来自PLAZA数据库5.0版（Van Bel et al. 2022）的植物HOMFAM或ORTHOFAM家族同源映射表数据，相关文件包括<plaza_v5_dicots_HOMFAM_orthomaps.tsv.zip>、<plaza_v5_dicots_ORTHOFAM_orthomaps.tsv.zip>、<plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip>以及<plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip>
