oggmap/orthomap - example data

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: Ensembl release-113 (-S last) Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-113 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: <ensembl_113_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_113_orthofinder_last_Orthogroups.tsv.zip> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <ensembl_113_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> OrthoFinder: WormBase release-WS293 + WormBase ParaSite release-WBPS19 (-S last) Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from WormBase release-WS293, WormBase ParaSite release-WBPS19 (keeping only longest isoforms): <WS293_WBPS19_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <WS293_WBPS19_orthofinder_last_Orthogroups.tsv.zip> Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: <WS293_WBPS19_orthofinder_last_species_list.tsv> Includes NCBI taxonomic tree for WormBase release-WS293 and WormBase ParaSite release-WBPS19 species analysed: <WS293_WBPS19_species_tree_ncbi_topology_named.nw> <WS293_WBPS19_species_tree_ncbi_topology_named.pdf> Broccoli: Example (default settings) Includes Broccoli results (default settings) for translated coding sequences (CDS) from four plant sepcies (keeping only longest isoforms) namely A. lyrata, A. thaliana, C. hirsuta and C. rubella: <broccoli_example_table_OGs_protein_counts.txt> <broccoli_example_table_OGs_protein_names.txt> Includes a table specifying the Broccoli species file names and its corresponding NCBI taxonomic IDs: <broccoli_example_species_list.tsv> 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; Ensembl-113): <Sun2021_Orthomap.tsv> <Cazet2022_Orthomap.tsv> <zebrafish_ensembl_105_orthomap.tsv> <zebrafish_ensembl_110_orthomap.tsv> <zebrafish_ensembl_113_orthomap.tsv> Pre-calculated Ensembl release-113 orthomaps (OrthoFinder -S last): Includes extracted orthomaps for all species from Ensembl release-113 based on OrthoFinder (-S last): <ensembl_113_orthofinder_last_orthomaps.zip> 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>本数据集为Python包oggmap/orthomap的示例数据。 OrthoFinder：Ensembl 版本105（参数：-S diamond_ultra_sens） 包含针对Ensembl版本105中所有翻译后的编码序列（Coding Sequence, CDS）（仅保留最长转录本异构体）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的OrthoFinder分析结果（参数：-S diamond_ultra_sens）： <ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip> <ensembl_105_orthofinder_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <ensembl_105_orthofinder_species_list.tsv> 包含本次分析所用Ensembl版本105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 版本110（参数：-S last） 包含针对Ensembl版本110中所有翻译后的编码序列（CDS）（仅保留最长转录本异构体）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的OrthoFinder分析结果（参数：-S last）： <ensembl_110_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_110_orthofinder_last_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <ensembl_110_orthofinder_last_species_list.tsv> 包含本次分析所用Ensembl版本110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 版本111（参数：-S last） 包含针对Ensembl版本111中所有翻译后的编码序列（CDS）（仅保留最长转录本异构体）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的OrthoFinder分析结果（参数：-S last）： <ensembl_111_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_111_orthofinder_last_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <ensembl_111_orthofinder_last_species_list.tsv> OrthoFinder：Ensembl 版本112（参数：-S last） 包含针对Ensembl版本112中所有翻译后的编码序列（CDS）（仅保留最长转录本异构体）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的OrthoFinder分析结果（参数：-S last）： <ensembl_112_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_112_orthofinder_last_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <ensembl_112_orthofinder_last_species_list.tsv> OrthoFinder：Ensembl 版本113（参数：-S last） 包含针对Ensembl版本113中所有翻译后的编码序列（CDS）（仅保留最长转录本异构体）以及来自www.xenbase.org的Xtropicalisv9.0.Named.primaryTrs.pep.fa的OrthoFinder分析结果（参数：-S last）： <ensembl_113_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <ensembl_113_orthofinder_last_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <ensembl_113_orthofinder_last_species_list.tsv> OrthoFinder：WormBase 版本WS288 + WormBase ParaSite 版本WBPS18（参数：-S last） 包含针对WormBase版本WS288、WormBase ParaSite版本WBPS18中所有翻译后的编码序列（CDS）（仅保留最长转录本异构体）以及来自https://planmine.mpibpc.mpg.de的dd_Smed_v6.pcf.contigs.fasta（经transdecoder和miniprothint预测的肽段序列）的OrthoFinder分析结果（参数：-S last）： <WS288_WBPS18_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <WS288_WBPS18_orthofinder_last_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <WS288_WBPS18_orthofinder_last_species_list.tsv> 包含本次分析所用WormBase版本WS288与WormBase ParaSite版本WBPS18物种的NCBI分类学树： <WS288_WBPS18_species_tree_ncbi_topology_named.nw> <WS288_WBPS18_species_tree_ncbi_topology_named.pdf> OrthoFinder：WormBase 版本WS293 + WormBase ParaSite 版本WBPS19（参数：-S last） 包含针对WormBase版本WS293、WormBase ParaSite版本WBPS19中所有翻译后的编码序列（CDS）（仅保留最长转录本异构体）的OrthoFinder分析结果（参数：-S last）： <WS293_WBPS19_orthofinder_last_Orthogroups.GeneCount.tsv.zip> <WS293_WBPS19_orthofinder_last_Orthogroups.tsv.zip> 包含一张表格，列明了OrthoFinder所用物种文件名及其对应的NCBI分类学ID： <WS293_WBPS19_orthofinder_last_species_list.tsv> 包含本次分析所用WormBase版本WS293与WormBase ParaSite版本WBPS19物种的NCBI分类学树： <WS293_WBPS19_species_tree_ncbi_topology_named.nw> <WS293_WBPS19_species_tree_ncbi_topology_named.pdf> Broccoli：默认参数示例 包含针对4种植物的翻译后编码序列（CDS）（仅保留最长转录本异构体）的Broccoli分析结果（默认参数），所涉物种包括A. lyrata、A. thaliana、C. hirsuta与C. rubella： <broccoli_example_table_OGs_protein_counts.txt> <broccoli_example_table_OGs_protein_names.txt> 包含一张表格，列明了Broccoli所用物种文件名及其对应的NCBI分类学ID： <broccoli_example_species_list.tsv> 预计算直系同源映射（orthomap）： 包含针对秀丽隐杆线虫（C. elegans，Sun等人2021年研究）、普通水螅（H. vulgaris，Cazet等人2022年研究）以及斑马鱼（D. rerio，对应Ensembl版本105、110、113）的预计算基因年龄分配结果： <Sun2021_Orthomap.tsv> <Cazet2022_Orthomap.tsv> <zebrafish_ensembl_105_orthomap.tsv> <zebrafish_ensembl_110_orthomap.tsv> <zebrafish_ensembl_113_orthomap.tsv> 预计算Ensembl版本113直系同源映射（基于OrthoFinder参数-S last）： 包含从Ensembl版本113中基于OrthoFinder（参数-S last）提取的所有物种的直系同源映射结果： <ensembl_113_orthofinder_last_orthomaps.zip> 预计算进化指数： 包含针对秀丽隐杆线虫（C. elegans，Ma等人2021年研究）的预计算进化指数，包括TajimaD、NormalizedPi、FayWu与Fst： <Ma2021_Fst.tsv> eggNOG数据库版本6.0直系同源映射： 包含从eggNOG数据库版本6.0（Hernández-Plaza等人2022年研究）中提取的所有真核生物的直系同源映射结果： <eggnog6_eukaryota_orthomaps.tsv.zip> myTAI示例数据： 包含来自myTAI R包（Drost等人2018年研究）的示例数据： <PhyloExpressionSetExample.h5ad> PLAZA数据库版本5.0直系同源映射： 包含从PLAZA数据库版本5.0（Van Bel等人2022年研究）中提取的植物HOMFAM或ORTHOFAM家族的直系同源映射结果： <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： 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）基因同义词表： <mouse_synonyms.tsv>