Based on the human cell cycle genes, the cell cycle genes of the corresponding species were captured by homologous gene conversion.
Usage
CycGenePrefetch(
species = "Homo_sapiens",
Ensembl_version = NULL,
mirror = NULL,
max_tries = 5,
use_cached_gene = TRUE,
verbose = TRUE
)Arguments
- species
Latin names for animals, i.e.,
"Homo_sapiens","Mus_musculus"- Ensembl_version
Ensembl database version. If NULL, use the current release version.
- mirror
Specify an Ensembl mirror to connect to. The valid options here are
"www","uswest","useast","asia".- max_tries
The maximum number of attempts to connect with the BioMart service.
- use_cached_gene
Whether to use previously cached cell cycle gene conversion results for the species. Default is
TRUE.- verbose
Whether to print the message. Default is
TRUE.
Examples
ccgenes <- CycGenePrefetch("Homo_sapiens")
#> ℹ [2025-09-20 13:08:25] Prefetching cell cycle genes for "Homo_sapiens" ...
#> ✔ [2025-09-20 13:08:25] Cell cycle gene prefetching completed "Homo_sapiens"
str(ccgenes)
#> List of 3
#> $ res: NULL
#> $ S : chr [1:43] "MCM5" "PCNA" "TYMS" "FEN1" ...
#> $ G2M: chr [1:54] "HMGB2" "CDK1" "NUSAP1" "UBE2C" ...
ccgenes <- CycGenePrefetch("Mus_musculus")
#> ℹ [2025-09-20 13:08:25] Prefetching cell cycle genes for "Mus_musculus" ...
#> ℹ [2025-09-20 13:08:25] Installing: biomaRt...
#>
#> → Will install 10 packages.
#> → All 10 packages (0 B) are cached.
#> + BiocFileCache 2.16.2 [bld]
#> + biomaRt 2.64.0 [bld]
#> + dbplyr 2.5.1
#> + filelock 1.0.3
#> + hms 1.1.3
#> + httr2 1.2.1
#> + prettyunits 1.2.0
#> + progress 1.2.3
#> + tidyr 1.3.1
#> + xml2 1.4.0 + ✔ libxml2-dev
#> ✔ All system requirements are already installed.
#>
#> ℹ No downloads are needed, 10 pkgs are cached
#> ✔ Got filelock 1.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (24.70 kB)
#> ✔ Got hms 1.1.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (99.70 kB)
#> ✔ Got progress 1.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (87.00 kB)
#> ✔ Got prettyunits 1.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (152.62 kB)
#> ✔ Got xml2 1.4.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (280.17 kB)
#> ✔ Got BiocFileCache 2.16.2 (source) (740.08 kB)
#> ✔ Got biomaRt 2.64.0 (source) (862.68 kB)
#> ✔ Got httr2 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (782.87 kB)
#> ✔ Got tidyr 1.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.18 MB)
#> ✔ Got dbplyr 2.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.24 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libxml2-dev libcurl4-openssl-dev libssl-dev libpng-dev libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.5).
#> libxml2-dev set to manually installed.
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.5).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
#> ✔ Installed dbplyr 2.5.1 (63ms)
#> ✔ Installed filelock 1.0.3 (78ms)
#> ✔ Installed hms 1.1.3 (99ms)
#> ✔ Installed httr2 1.2.1 (130ms)
#> ✔ Installed prettyunits 1.2.0 (60ms)
#> ✔ Installed progress 1.2.3 (103ms)
#> ✔ Installed tidyr 1.3.1 (68ms)
#> ℹ Building BiocFileCache 2.16.2
#> ✔ Installed xml2 1.4.0 (77ms)
#> ✔ Built BiocFileCache 2.16.2 (3.8s)
#> ✔ Installed BiocFileCache 2.16.2 (32ms)
#> ℹ Building biomaRt 2.64.0
#> ✔ Built biomaRt 2.64.0 (7.8s)
#> ✔ Installed biomaRt 2.64.0 (1s)
#> ✔ 1 pkg + 57 deps: kept 48, added 10, dld 10 (5.45 MB) [17.4s]
#> ℹ [2025-09-20 13:08:43] biomaRt installed successfully
#> ℹ [2025-09-20 13:08:43] Connect to the Ensembl archives...
#> ℹ [2025-09-20 13:08:44] Using the "115" version of biomart...
#> ℹ [2025-09-20 13:08:44] Downloading the biomart from "https://sep2025.archive.ensembl.org"...
#> ℹ [2025-09-20 13:08:46] Searching the dataset "hsapiens" ...
#> ℹ [2025-09-20 13:08:47] Connecting to the dataset hsapiens_gene_ensembl ...
#> ℹ [2025-09-20 13:08:48] Converting the geneIDs...
#> ℹ [2025-09-20 13:08:49] 97 genes mapped with "ensembl_symbol"
#> ℹ [2025-09-20 13:08:49] ==============================
#> ℹ 97 genes mapped
#> ℹ 0 genes unmapped
#> ℹ ==============================
#> ℹ [2025-09-20 13:08:49] Cached conversion results for "Mus_musculus"
#> ✔ [2025-09-20 13:08:49] Cell cycle gene prefetching completed "Mus_musculus"
str(ccgenes)
#> List of 3
#> $ res:List of 7
#> ..$ geneID_res :'data.frame': 100 obs. of 4 variables:
#> .. ..$ from_IDtype: chr [1:100] "ensembl_symbol" "ensembl_symbol" "ensembl_symbol" "ensembl_symbol" ...
#> .. ..$ from_geneID: chr [1:100] "NCAPD2" "ANLN" "UBR7" "TACC3" ...
#> .. ..$ to_IDtype : chr [1:100] "symbol" "symbol" "symbol" "symbol" ...
#> .. ..$ to_geneID : chr [1:100] "Ncapd2" "Anln" "Ubr7" "Tacc3" ...
#> ..$ geneID_collapse:'data.frame': 96 obs. of 2 variables:
#> .. ..$ from_geneID: chr [1:96] "ANLN" "ANP32E" "ATAD2" "AURKA" ...
#> .. ..$ symbol :List of 96
#> .. .. ..$ : chr "Anln"
#> .. .. ..$ : chr "Anp32e"
#> .. .. ..$ : chr "Atad2"
#> .. .. ..$ : chr "Aurka"
#> .. .. ..$ : chr "Aurkb"
#> .. .. ..$ : chr "Birc5"
#> .. .. ..$ : chr "Blm"
#> .. .. ..$ : chr "Bub1"
#> .. .. ..$ : chr "Casp8ap2"
#> .. .. ..$ : chr "Cbx5"
#> .. .. ..$ : chr "Ccnb2"
#> .. .. ..$ : chr "Ccne2"
#> .. .. ..$ : chr "Cdc20"
#> .. .. ..$ : chr "Cdc25c"
#> .. .. ..$ : chr "Cdc45"
#> .. .. ..$ : chr "Cdc6"
#> .. .. ..$ : chr "Cdca2"
#> .. .. ..$ : chr "Cdca3"
#> .. .. ..$ : chr "Cdca7"
#> .. .. ..$ : chr "Cdca8"
#> .. .. ..$ : chr "Cdk1"
#> .. .. ..$ : chr "Cenpa"
#> .. .. ..$ : chr "Cenpe"
#> .. .. ..$ : chr "Cenpf"
#> .. .. ..$ : chr "Cenpu"
#> .. .. ..$ : chr "Chaf1b"
#> .. .. ..$ : chr "Ckap2"
#> .. .. ..$ : chr "Ckap2l"
#> .. .. ..$ : chr "Ckap5"
#> .. .. ..$ : chr [1:2] "Cks1brt" "Cks1b"
#> .. .. ..$ : chr "Cks2"
#> .. .. ..$ : chr "Clspn"
#> .. .. ..$ : chr "Ctcf"
#> .. .. ..$ : chr "Dlgap5"
#> .. .. ..$ : chr "Dscc1"
#> .. .. ..$ : chr "Dtl"
#> .. .. ..$ : chr "E2f8"
#> .. .. ..$ : chr "Ect2"
#> .. .. ..$ : chr "Exo1"
#> .. .. ..$ : chr "Fen1"
#> .. .. ..$ : chr "G2e3"
#> .. .. ..$ : chr "Gas2l3"
#> .. .. ..$ : chr "Gins2"
#> .. .. ..$ : chr "Gmnn"
#> .. .. ..$ : chr "Gtse1"
#> .. .. ..$ : chr "Hells"
#> .. .. ..$ : chr "Hjurp"
#> .. .. ..$ : chr "Hmgb2"
#> .. .. ..$ : chr "Hmmr"
#> .. .. ..$ : chr "Jpt1"
#> .. .. ..$ : chr "Kif11"
#> .. .. ..$ : chr "Kif20b"
#> .. .. ..$ : chr "Kif23"
#> .. .. ..$ : chr "Kif2c"
#> .. .. ..$ : chr "Lbr"
#> .. .. ..$ : chr "Mcm4"
#> .. .. ..$ : chr "Mcm5"
#> .. .. ..$ : chr "Mcm6"
#> .. .. ..$ : chr "Mcm7"
#> .. .. ..$ : chr "Mki67"
#> .. .. ..$ : chr "Mrpl36"
#> .. .. ..$ : chr "Msh2"
#> .. .. ..$ : chr "Nasp"
#> .. .. ..$ : chr "Ncapd2"
#> .. .. ..$ : chr "Ndc80"
#> .. .. ..$ : chr "Nek2"
#> .. .. ..$ : chr "Nuf2"
#> .. .. ..$ : chr "Nusap1"
#> .. .. ..$ : chr "Pcna"
#> .. .. ..$ : chr "Pimreg"
#> .. .. ..$ : chr "Pola1"
#> .. .. ..$ : chr "Polr1b"
#> .. .. ..$ : chr "Prim1"
#> .. .. ..$ : chr "Psrc1"
#> .. .. ..$ : chr "Rad51"
#> .. .. ..$ : chr "Rad51ap1"
#> .. .. ..$ : chr "Rangap1"
#> .. .. ..$ : chr "Rfc2"
#> .. .. ..$ : chr "Rrm1"
#> .. .. ..$ : chr "Rrm2"
#> .. .. ..$ : chr "Slbp"
#> .. .. ..$ : chr "Smc4"
#> .. .. ..$ : chr "Tacc3"
#> .. .. ..$ : chr "Tipin"
#> .. .. ..$ : chr "Tmpo"
#> .. .. ..$ : chr "Top2a"
#> .. .. ..$ : chr "Tpx2"
#> .. .. ..$ : chr "Ttk"
#> .. .. ..$ : chr "Tubb4b"
#> .. .. ..$ : chr "Tyms"
#> .. .. ..$ : chr "Ube2c"
#> .. .. ..$ : chr "Ubr7"
#> .. .. ..$ : chr "Uhrf1"
#> .. .. ..$ : chr "Ung"
#> .. .. ..$ : chr "Usp1"
#> .. .. ..$ : chr "Wdr76"
#> .. .. ..- attr(*, "class")= chr "AsIs"
#> ..$ geneID_expand :'data.frame': 97 obs. of 2 variables:
#> .. ..$ from_geneID: chr [1:97] "ANLN" "ANP32E" "ATAD2" "AURKA" ...
#> .. ..$ symbol : chr [1:97] "Anln" "Anp32e" "Atad2" "Aurka" ...
#> ..$ Ensembl_version: chr "115"
#> ..$ Datasets :'data.frame': 213 obs. of 3 variables:
#> .. ..$ dataset : 'AsIs' chr [1:213] "abrachyrhynchus_gene_ensembl" "acalliptera_gene_ensembl" "acarolinensis_gene_ensembl" "acchrysaetos_gene_ensembl" ...
#> .. ..$ description: 'AsIs' chr [1:213] "Pink-footed goose genes (ASM259213v1)" "Eastern happy genes (fAstCal1.3)" "Green anole genes (AnoCar2.0v2)" "Golden eagle genes (bAquChr1.2)" ...
#> .. ..$ version : 'AsIs' chr [1:213] "ASM259213v1" "fAstCal1.3" "AnoCar2.0v2" "bAquChr1.2" ...
#> ..$ Attributes :'data.frame': 3170 obs. of 3 variables:
#> .. ..$ name : chr [1:3170] "ensembl_gene_id" "ensembl_gene_id_version" "ensembl_transcript_id" "ensembl_transcript_id_version" ...
#> .. ..$ description: chr [1:3170] "Gene stable ID" "Gene stable ID version" "Transcript stable ID" "Transcript stable ID version" ...
#> .. ..$ page : chr [1:3170] "feature_page" "feature_page" "feature_page" "feature_page" ...
#> ..$ geneID_unmapped: chr(0)
#> $ S : chr [1:42] "Mcm5" "Pcna" "Tyms" "Fen1" ...
#> $ G2M: chr [1:55] "Hmgb2" "Cdk1" "Nusap1" "Ube2c" ...