Files in Bioconductor/GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

DESCRIPTION

NAMESPACE

NEWS

R/Ensembl-utils.R R/GenomeDescription-class.R R/NCBI-utils.R R/Seqinfo-class.R R/UCSC-utils.R R/fetch_table_dump_from_Ensembl_FTP.R R/getChromInfoFromEnsembl.R R/getChromInfoFromNCBI.R R/getChromInfoFromUCSC.R R/list_ftp_dir.R R/loadTaxonomyDb.R R/mapGenomeBuilds.R R/rankSeqlevels.R R/seqinfo.R R/seqlevels-wrappers.R R/seqlevelsStyle.R R/utils.R R/zzz.R README.md

inst/extdata/assembled_molecules_db/UCSC/README.TXT

inst/extdata/assembled_molecules_db/UCSC/bosTau7.tab

inst/extdata/assembled_molecules_db/UCSC/bosTau8.tab

inst/extdata/assembled_molecules_db/UCSC/bosTau9.tab

inst/extdata/assembled_molecules_db/UCSC/canFam4.tab

inst/extdata/assembled_molecules_db/UCSC/canFam5.tab

inst/extdata/assembled_molecules_db/UCSC/canFam6.tab

inst/extdata/assembled_molecules_db/UCSC/ce10.tab

inst/extdata/assembled_molecules_db/UCSC/ce11.tab

inst/extdata/assembled_molecules_db/UCSC/danRer10.tab

inst/extdata/assembled_molecules_db/UCSC/danRer11.tab

inst/extdata/assembled_molecules_db/UCSC/dm3.tab

inst/extdata/assembled_molecules_db/UCSC/dm6.tab

inst/extdata/assembled_molecules_db/UCSC/felCat9.tab

inst/extdata/assembled_molecules_db/UCSC/galGal4.tab

inst/extdata/assembled_molecules_db/UCSC/galGal5.tab

inst/extdata/assembled_molecules_db/UCSC/galGal6.tab

inst/extdata/assembled_molecules_db/UCSC/gorGor6.tab

inst/extdata/assembled_molecules_db/UCSC/hg18.tab

inst/extdata/assembled_molecules_db/UCSC/hg19.tab

inst/extdata/assembled_molecules_db/UCSC/hg38.tab

inst/extdata/assembled_molecules_db/UCSC/hs1.tab

inst/extdata/assembled_molecules_db/UCSC/mm10.tab

inst/extdata/assembled_molecules_db/UCSC/mm39.tab

inst/extdata/assembled_molecules_db/UCSC/mm9.tab

inst/extdata/assembled_molecules_db/UCSC/panTro4.tab

inst/extdata/assembled_molecules_db/UCSC/panTro5.tab

inst/extdata/assembled_molecules_db/UCSC/panTro6.tab

inst/extdata/assembled_molecules_db/UCSC/rheMac10.tab

inst/extdata/assembled_molecules_db/UCSC/rheMac8.tab

inst/extdata/assembled_molecules_db/UCSC/rn6.tab

inst/extdata/assembled_molecules_db/UCSC/rn7.tab

inst/extdata/assembled_molecules_db/UCSC/xenLae2.tab

inst/extdata/assembled_molecules_db/UCSC/xenTro10.tab

inst/extdata/assembly_accessions.rda

inst/extdata/dataFiles/Arabidopsis_thaliana.txt

inst/extdata/dataFiles/Caenorhabditis_elegans.txt

inst/extdata/dataFiles/Canis_familiaris.txt

inst/extdata/dataFiles/Cyanidioschyzon_merolae.txt

inst/extdata/dataFiles/Drosophila_melanogaster.txt

inst/extdata/dataFiles/Gossypium_hirsutum.txt

inst/extdata/dataFiles/Homo_sapiens.txt

inst/extdata/dataFiles/Mus_musculus.txt

inst/extdata/dataFiles/Oryza_sativa.txt

inst/extdata/dataFiles/Populus_trichocarpa.txt

inst/extdata/dataFiles/README

inst/extdata/dataFiles/Rattus_norvegicus.txt

inst/extdata/dataFiles/Saccharomyces_cerevisiae.txt

inst/extdata/dataFiles/Zea_mays.txt

inst/extdata/dataFiles/genomeMappingTbl.csv

inst/registered/NCBI_assemblies/Acyrthosiphon_pisum.R inst/registered/NCBI_assemblies/Ambystoma_mexicanum.R inst/registered/NCBI_assemblies/Apis_mellifera.R inst/registered/NCBI_assemblies/Arabidopsis_thaliana.R inst/registered/NCBI_assemblies/Betacoronavirus.R inst/registered/NCBI_assemblies/Bos_taurus.R inst/registered/NCBI_assemblies/Brassica_napus.R inst/registered/NCBI_assemblies/Caenorhabditis_elegans.R inst/registered/NCBI_assemblies/Callithrix_jacchus.R inst/registered/NCBI_assemblies/Camponotus_floridanus.R inst/registered/NCBI_assemblies/Canis_lupus_familiaris.R inst/registered/NCBI_assemblies/Cannabis_sativa.R inst/registered/NCBI_assemblies/Catharus_ustulatus.R inst/registered/NCBI_assemblies/Cavia_porcellus.R inst/registered/NCBI_assemblies/Chlamydomonas_reinhardtii.R inst/registered/NCBI_assemblies/Danio_rerio.R inst/registered/NCBI_assemblies/Drosophila_melanogaster.R inst/registered/NCBI_assemblies/Drosophila_virilis.R inst/registered/NCBI_assemblies/Equus_caballus.R inst/registered/NCBI_assemblies/Escherichia_coli.R inst/registered/NCBI_assemblies/Eucalyptus_grandis.R inst/registered/NCBI_assemblies/Felis_catus.R inst/registered/NCBI_assemblies/Fundulus_heteroclitus.R inst/registered/NCBI_assemblies/Galleria_mellonella.R inst/registered/NCBI_assemblies/Gallus_gallus.R inst/registered/NCBI_assemblies/Gasterosteus_aculeatus.R inst/registered/NCBI_assemblies/Glycine_max.R inst/registered/NCBI_assemblies/Gorilla_gorilla_gorilla.R inst/registered/NCBI_assemblies/Gossypium_hirsutum.R inst/registered/NCBI_assemblies/Harpegnathos_saltator.R inst/registered/NCBI_assemblies/Homo_sapiens.R inst/registered/NCBI_assemblies/Hordeum_vulgare.R inst/registered/NCBI_assemblies/Loxodonta_africana.R inst/registered/NCBI_assemblies/Macaca_fascicularis.R inst/registered/NCBI_assemblies/Macaca_mulatta.R inst/registered/NCBI_assemblies/Madurella_mycetomatis.R inst/registered/NCBI_assemblies/Microtus_ochrogaster.R inst/registered/NCBI_assemblies/Monodelphis_domestica.R inst/registered/NCBI_assemblies/Mus_musculus.R inst/registered/NCBI_assemblies/Mustela_putorius_furo.R inst/registered/NCBI_assemblies/Pan_paniscus.R inst/registered/NCBI_assemblies/Pan_troglodytes.R inst/registered/NCBI_assemblies/Patiria_miniata.R inst/registered/NCBI_assemblies/Petromyzon_marinus.R inst/registered/NCBI_assemblies/Plasmodium_falciparum.R inst/registered/NCBI_assemblies/Pteropus_alecto.R inst/registered/NCBI_assemblies/Rattus_norvegicus.R inst/registered/NCBI_assemblies/Saccharomyces_cerevisiae.R inst/registered/NCBI_assemblies/Salmo_salar.R inst/registered/NCBI_assemblies/Strigops_habroptila.R inst/registered/NCBI_assemblies/Sus_scrofa.R inst/registered/NCBI_assemblies/Taeniopygia_guttata.R inst/registered/NCBI_assemblies/Triticum_aestivum.R inst/registered/NCBI_assemblies/Vitis_vinifera.R inst/registered/NCBI_assemblies/Xenopus_laevis.R inst/registered/NCBI_assemblies/Xenopus_tropicalis.R

inst/registered/UCSC_genomes/README.TXT

inst/registered/UCSC_genomes/apiMel1.R inst/registered/UCSC_genomes/apiMel2.R inst/registered/UCSC_genomes/bosTau1.R inst/registered/UCSC_genomes/bosTau2.R inst/registered/UCSC_genomes/bosTau3.R inst/registered/UCSC_genomes/bosTau4.R inst/registered/UCSC_genomes/bosTau6.R inst/registered/UCSC_genomes/bosTau7.R inst/registered/UCSC_genomes/bosTau8.R inst/registered/UCSC_genomes/bosTau9.R inst/registered/UCSC_genomes/calJac3.R inst/registered/UCSC_genomes/calJac4.R inst/registered/UCSC_genomes/canFam1.R inst/registered/UCSC_genomes/canFam2.R inst/registered/UCSC_genomes/canFam3.R inst/registered/UCSC_genomes/canFam4.R inst/registered/UCSC_genomes/canFam5.R inst/registered/UCSC_genomes/canFam6.R inst/registered/UCSC_genomes/ce10.R inst/registered/UCSC_genomes/ce11.R inst/registered/UCSC_genomes/ce2.R inst/registered/UCSC_genomes/ce4.R inst/registered/UCSC_genomes/ce6.R inst/registered/UCSC_genomes/danRer10.R inst/registered/UCSC_genomes/danRer11.R inst/registered/UCSC_genomes/danRer5.R inst/registered/UCSC_genomes/danRer6.R inst/registered/UCSC_genomes/danRer7.R inst/registered/UCSC_genomes/dm1.R inst/registered/UCSC_genomes/dm2.R inst/registered/UCSC_genomes/dm3.R inst/registered/UCSC_genomes/dm6.R inst/registered/UCSC_genomes/eboVir3.R inst/registered/UCSC_genomes/equCab1.R inst/registered/UCSC_genomes/equCab2.R inst/registered/UCSC_genomes/equCab3.R inst/registered/UCSC_genomes/felCat9.R inst/registered/UCSC_genomes/galGal2.R inst/registered/UCSC_genomes/galGal3.R inst/registered/UCSC_genomes/galGal4.R inst/registered/UCSC_genomes/galGal5.R inst/registered/UCSC_genomes/galGal6.R inst/registered/UCSC_genomes/gasAcu1.R inst/registered/UCSC_genomes/gorGor6.R inst/registered/UCSC_genomes/hg15.R inst/registered/UCSC_genomes/hg16.R inst/registered/UCSC_genomes/hg17.R inst/registered/UCSC_genomes/hg18.R inst/registered/UCSC_genomes/hg19.R inst/registered/UCSC_genomes/hg38.R inst/registered/UCSC_genomes/hs1.R inst/registered/UCSC_genomes/loxAfr3.R inst/registered/UCSC_genomes/macFas5.R inst/registered/UCSC_genomes/mm10.R inst/registered/UCSC_genomes/mm39.R inst/registered/UCSC_genomes/mm8.R inst/registered/UCSC_genomes/mm9.R inst/registered/UCSC_genomes/monDom5.R inst/registered/UCSC_genomes/mpxvRivers.R inst/registered/UCSC_genomes/musFur1.R inst/registered/UCSC_genomes/panPan1.R inst/registered/UCSC_genomes/panPan2.R inst/registered/UCSC_genomes/panPan3.R inst/registered/UCSC_genomes/panTro1.R inst/registered/UCSC_genomes/panTro2.R inst/registered/UCSC_genomes/panTro3.R inst/registered/UCSC_genomes/panTro4.R inst/registered/UCSC_genomes/panTro5.R inst/registered/UCSC_genomes/panTro6.R inst/registered/UCSC_genomes/rheMac10.R inst/registered/UCSC_genomes/rheMac2.R inst/registered/UCSC_genomes/rheMac3.R inst/registered/UCSC_genomes/rheMac8.R inst/registered/UCSC_genomes/rn1.R inst/registered/UCSC_genomes/rn2.R inst/registered/UCSC_genomes/rn3.R inst/registered/UCSC_genomes/rn4.R inst/registered/UCSC_genomes/rn5.R inst/registered/UCSC_genomes/rn6.R inst/registered/UCSC_genomes/rn7.R inst/registered/UCSC_genomes/sacCer1.R inst/registered/UCSC_genomes/sacCer2.R inst/registered/UCSC_genomes/sacCer3.R inst/registered/UCSC_genomes/susScr11.R inst/registered/UCSC_genomes/susScr2.R inst/registered/UCSC_genomes/susScr3.R inst/registered/UCSC_genomes/taeGut1.R inst/registered/UCSC_genomes/taeGut2.R inst/registered/UCSC_genomes/wuhCor1.R inst/registered/UCSC_genomes/xenLae2.R inst/registered/UCSC_genomes/xenTro10.R inst/unitTests/test_Seqinfo-class.R inst/unitTests/test_mapGenomeBuilds.R inst/unitTests/test_rankSeqlevels.R inst/unitTests/test_seqlevels-wrappers.R inst/unitTests/test_seqlevelsStyle.R inst/unitTests/test_utils.R man/GenomeDescription-class.Rd man/GenomeInfoDb-internals.Rd man/NCBI-utils.Rd man/Seqinfo-class.Rd man/getChromInfoFromEnsembl.Rd man/getChromInfoFromNCBI.Rd man/getChromInfoFromUCSC.Rd man/loadTaxonomyDb.Rd man/mapGenomeBuilds.Rd man/rankSeqlevels.Rd man/seqinfo.Rd man/seqlevels-wrappers.Rd man/seqlevelsStyle.Rd tests/run_unitTests.R vignettes/Accept-organism-for-GenomeInfoDb.Rmd

vignettes/GenomeInfoDb.Rnw

Bioconductor/GenomeInfoDb documentation built on April 19, 2024, 9:28 a.m.