oggmap/orthomap - example data
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Example data for python package oggmap/orthomap. OrthoFinder: Ensembl release-105 (-S diamond_ultra_sens) Includes OrthoFinder results (-S diamond_ultra_sens) 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.tsv.zip> 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> OrthoFinder: Ensembl release-110 (-S last) Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-110 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: <ensembl_110_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_110_orthofinder_last_Orthogroups.tsv.zip> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <ensembl_110_orthofinder_last_species_list.tsv> Includes NCBI taxonomic tree for Ensembl release-110 species analysed: <ensembl_110_species_tree_ncbi_topology_named.nw> <ensembl_110_species_tree_ncbi_topology_named.pdf> OrthoFinder: Ensembl release-111 (-S last) Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-111 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: <ensembl_111_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_111_orthofinder_last_Orthogroups.tsv.zip> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <ensembl_111_orthofinder_last_species_list.tsv> OrthoFinder: Ensembl release-112 (-S last) Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-112 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: <ensembl_112_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_112_orthofinder_last_Orthogroups.tsv.zip> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <ensembl_112_orthofinder_last_species_list.tsv> OrthoFinder: WormBase release-WS288 + WormBase ParaSite release-WBPS18 (-S last) Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from WormBase release-WS288, WormBase ParaSite release-WBPS18 (keeping only longest isoforms) and dd_Smed_v6.pcf.contigs.fasta (transdecoder and miniprothint peptides) from https://planmine.mpibpc.mpg.de: <WS288_WBPS18_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <WS288_WBPS18_orthofinder_last_Orthogroups.tsv.zip> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <WS288_WBPS18_orthofinder_last_species_list.tsv> Includes NCBI taxonomic tree for WormBase release-WS288 and WormBase ParaSite release-WBPS18 species analysed: <WS288_WBPS18_species_tree_ncbi_topology_named.nw> <WS288_WBPS18_species_tree_ncbi_topology_named.pdf> Pre-calculated orthomaps: Includes pre-calculated gene age assignments for C. elegans (Sun et al. 2021), H. vulgaris (Cazet et al. 2022) and D. rerio (Ensembl-105; Ensembl-110): <Sun2021_Orthomap.tsv> <Cazet2022_Orthomap.tsv> <zebrafish_ensembl_105_orthomap.tsv> <zebrafish_ensembl_110_orthomap.tsv> Pre-calculated evolutionary indices: Includes pre-calculated TajimaD, NormalizedPi, FayWu, Fst for C. elegans (Ma et al. 2021): <Ma2021_Fst.tsv> eggNOG database version 6.0 orthomaps: Includes extracted orthomaps for all Eukaryota from eggNOG database version 6.0 (Hernández-Plaza et al. 2022): <eggnog6_eukaryota_orthomaps.tsv.zip> myTAI example data: Includes example data from the myTAI R package (Drost et al. 2018) <PhyloExpressionSetExample.h5ad> PLAZA database version 5.0 orthomaps: 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> Mouse synonyms: Table of Mus musculus gene synonyms obtained from here https://github.com/mustafapir/geneName/blob/master/data/mouse_synonyms1.rda and converted into a table. <mouse_synonyms.tsv>
适用于Python包oggmap/orthomap的示例数据集。 OrthoFinder：Ensembl数据库（Ensembl）release-105（参数：-S diamond_ultra_sens） 本数据集包含针对Ensembl数据库release-105版本（仅保留最长转录本）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的所有翻译编码序列（Coding Sequence，CDS）所生成的OrthoFinder分析结果（采用参数-S diamond_ultra_sens）： <ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip> <ensembl_105_orthofinder_Orthogroups.tsv.zip> 本数据集还包含一张表格，用于指定OrthoFinder所用物种文件名及其对应的NCBI分类学标识符： <ensembl_105_orthofinder_species_list.tsv> 本数据集包含本次分析所用Ensembl数据库release-105版本物种的NCBI分类学树： <ensembl_105_species_tree_ncbi_topology_named.nw> <ensembl_105_species_tree_ncbi_topology_named.pdf> OrthoFinder：Ensembl数据库（Ensembl）release-110（参数：-S last） 本数据集包含针对Ensembl数据库release-110版本（仅保留最长转录本）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的所有翻译编码序列（Coding Sequence，CDS）所生成的OrthoFinder分析结果（采用参数-S last）： <ensembl_110_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_110_orthofinder_last_Orthogroups.tsv.zip> 本数据集还包含一张表格，用于指定OrthoFinder所用物种文件名及其对应的NCBI分类学标识符： <ensembl_110_orthofinder_last_species_list.tsv> 本数据集包含本次分析所用Ensembl数据库release-110版本物种的NCBI分类学树： <ensembl_110_species_tree_ncbi_topology_named.nw> <ensembl_110_species_tree_ncbi_topology_named.pdf> OrthoFinder：Ensembl数据库（Ensembl）release-111（参数：-S last） 本数据集包含针对Ensembl数据库release-111版本（仅保留最长转录本）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的所有翻译编码序列（Coding Sequence，CDS）所生成的OrthoFinder分析结果（采用参数-S last）： <ensembl_111_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_111_orthofinder_last_Orthogroups.tsv.zip> 本数据集还包含一张表格，用于指定OrthoFinder所用物种文件名及其对应的NCBI分类学标识符： <ensembl_111_orthofinder_last_species_list.tsv> OrthoFinder：Ensembl数据库（Ensembl）release-112（参数：-S last） 本数据集包含针对Ensembl数据库release-112版本（仅保留最长转录本）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的所有翻译编码序列（Coding Sequence，CDS）所生成的OrthoFinder分析结果（采用参数-S last）： <ensembl_112_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_112_orthofinder_last_Orthogroups.tsv.zip> 本数据集还包含一张表格，用于指定OrthoFinder所用物种文件名及其对应的NCBI分类学标识符： <ensembl_112_orthofinder_last_species_list.tsv> OrthoFinder：WormBase数据库（WormBase）release-WS288 + WormBase ParaSite数据库release-WBPS18（参数：-S last） 本数据集包含针对WormBase数据库release-WS288版本、WormBase ParaSite数据库release-WBPS18版本（仅保留最长转录本）以及来自https://planmine.mpibpc.mpg.de的dd_Smed_v6.pcf.contigs.fasta（经TransDecoder和Miniprothint预测的肽序列）所生成的OrthoFinder分析结果（采用参数-S last）： <WS288_WBPS18_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <WS288_WBPS18_orthofinder_last_Orthogroups.tsv.zip> 本数据集还包含一张表格，用于指定OrthoFinder所用物种文件名及其对应的NCBI分类学标识符： <WS288_WBPS18_orthofinder_last_species_list.tsv> 本数据集包含本次分析所用WormBase数据库release-WS288与WormBase ParaSite数据库release-WBPS18版本物种的NCBI分类学树： <WS288_WBPS18_species_tree_ncbi_topology_named.nw> <WS288_WBPS18_species_tree_ncbi_topology_named.pdf> 预计算直系同源映射（orthomap） 本数据集包含秀丽隐杆线虫（C. elegans，Sun et al. 2021）、水螅（H. vulgaris，Cazet et al. 2022）以及斑马鱼（D. rerio，对应Ensembl-105、Ensembl-110版本）的预计算基因年龄赋值数据： <Sun2021_Orthomap.tsv> <Cazet2022_Orthomap.tsv> <zebrafish_ensembl_105_orthomap.tsv> <zebrafish_ensembl_110_orthomap.tsv> 预计算进化指数 本数据集包含秀丽隐杆线虫（Ma et al. 2021）的预计算塔吉玛D统计量（TajimaD）、标准化核苷酸多样性（NormalizedPi）、费伊吴统计量（FayWu）以及群体分化指数（Fst）： <Ma2021_Fst.tsv> eggNOG数据库v6.0直系同源映射 本数据集包含从eggNOG数据库v6.0（Hernández-Plaza et al. 2022）中提取的所有真核生物直系同源映射数据： <eggnog6_eukaryota_orthomaps.tsv.zip> myTAI示例数据集 本数据集包含来自myTAI R包（Drost et al. 2018）的示例数据： <PhyloExpressionSetExample.h5ad> PLAZA数据库v5.0直系同源映射 本数据集包含从PLAZA数据库v5.0（Van Bel et al. 2022）中提取的植物HOMFAM或ORTHOFAM家族的直系同源映射数据： <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> 小鼠基因同义词表 本数据集包含从https://github.com/mustafapir/geneName/blob/master/data/mouse_synonyms1.rda获取并转换为表格形式的小家鼠（Mus musculus）基因同义词数据： <mouse_synonyms.tsv>
