AHLRBaseDbs 1.6.0
Authors: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Last modified: 2023-03-28 14:08:49.234662
Compiled: Tue Mar 28 14:10:44 2023
To install this package, start R (>= 4.1.0) and enter:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AHLRBaseDbs")LRBaseDb databases from AnnotationHubThe AHLRBaseDbs package provides the metadata for all LRBaseDb SQLite
databases in AnnotationHub.
First we load/update the AnnotationHub resource.
library(AnnotationHub)
ah <- AnnotationHub()Next we list all LRBaseDb entries from AnnotationHub.
query(ah, "LRBaseDb")## AnnotationHub with 625 records
## # snapshotDate(): 2023-03-28
## # $dataprovider: FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CE...
## # $species: Xenopus tropicalis, Vulpes vulpes, Ursus maritimus, Takifugu rub...
## # $rdataclass: SQLiteFile
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH91646"]]'
##
## title
## AH91646 | LRBaseDb for Anolis carolinensis (Anole lizard, v001)
## AH91647 | LRBaseDb for Aquila chrysaetos chrysaetos (Golden eagle, v001)
## AH91648 | LRBaseDb for Astatotilapia calliptera (Eastern happy, v001)
## AH91649 | LRBaseDb for Anopheles gambiae str. PEST (Anopheline, v001)
## AH91650 | LRBaseDb for Ailuropoda melanoleuca (Panda, v001)
## ... ...
## AH111454 | LRBaseDb for Taeniopygia guttata (Zebra finch, v005)
## AH111455 | LRBaseDb for Takifugu rubripes (Fugu, v005)
## AH111456 | LRBaseDb for Ursus maritimus (Polar bear, v005)
## AH111457 | LRBaseDb for Vulpes vulpes (Red fox, v005)
## AH111458 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v005)We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket
with mcols().
mcols(query(ah, "LRBaseDb"))## DataFrame with 625 rows and 15 columns
## title dataprovider species
## <character> <character> <character>
## AH91646 LRBaseDb for Anolis .. FANTOM5,DLRP,IUPHAR,.. Anolis carolinensis
## AH91647 LRBaseDb for Aquila .. FANTOM5,DLRP,IUPHAR,.. Aquila chrysaetos ch..
## AH91648 LRBaseDb for Astatot.. FANTOM5,DLRP,IUPHAR,.. Astatotilapia callip..
## AH91649 LRBaseDb for Anophel.. FANTOM5,DLRP,IUPHAR,.. Anopheles gambiae st..
## AH91650 LRBaseDb for Ailurop.. FANTOM5,DLRP,IUPHAR,.. Ailuropoda melanoleuca
## ... ... ... ...
## AH111454 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,.. Taeniopygia guttata
## AH111455 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,.. Takifugu rubripes
## AH111456 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,.. Ursus maritimus
## AH111457 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,.. Vulpes vulpes
## AH111458 LRBaseDb for Xenopus.. FANTOM5,DLRP,IUPHAR,.. Xenopus tropicalis
## taxonomyid genome description coordinate_1_based
## <integer> <character> <character> <integer>
## AH91646 28377 NA Correspondence table.. 1
## AH91647 223781 NA Correspondence table.. 1
## AH91648 8154 NA Correspondence table.. 1
## AH91649 180454 NA Correspondence table.. 1
## AH91650 9646 NA Correspondence table.. 1
## ... ... ... ... ...
## AH111454 59729 NA Correspondence table.. 1
## AH111455 31033 NA Correspondence table.. 1
## AH111456 29073 NA Correspondence table.. 1
## AH111457 9627 NA Correspondence table.. 1
## AH111458 8364 NA Correspondence table.. 1
## maintainer rdatadateadded preparerclass
## <character> <character> <character>
## AH91646 Koki Tsuyuzaki <k.t... 2021-04-19 AHLRBaseDbs
## AH91647 Koki Tsuyuzaki <k.t... 2021-04-19 AHLRBaseDbs
## AH91648 Koki Tsuyuzaki <k.t... 2021-04-19 AHLRBaseDbs
## AH91649 Koki Tsuyuzaki <k.t... 2021-04-19 AHLRBaseDbs
## AH91650 Koki Tsuyuzaki <k.t... 2021-04-19 AHLRBaseDbs
## ... ... ... ...
## AH111454 Koki Tsuyuzaki <k.t... 2023-03-28 AHLRBaseDbs
## AH111455 Koki Tsuyuzaki <k.t... 2023-03-28 AHLRBaseDbs
## AH111456 Koki Tsuyuzaki <k.t... 2023-03-28 AHLRBaseDbs
## AH111457 Koki Tsuyuzaki <k.t... 2023-03-28 AHLRBaseDbs
## AH111458 Koki Tsuyuzaki <k.t... 2023-03-28 AHLRBaseDbs
## tags rdataclass
## <AsIs> <character>
## AH91646 Annotation,Anole lizard,Anolis carolinensis,... SQLiteFile
## AH91647 Annotation,Aquila chrysaetos ch..,BADERLAB,... SQLiteFile
## AH91648 Annotation,Astatotilapia callip..,BADERLAB,... SQLiteFile
## AH91649 Annotation,Anopheles gambiae st..,Anopheline,... SQLiteFile
## AH91650 Ailuropoda melanoleuca,Annotation,BADERLAB,... SQLiteFile
## ... ... ...
## AH111454 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH111455 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH111456 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH111457 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH111458 Annotation,BADERLAB,BIOMART,... SQLiteFile
## rdatapath sourceurl sourcetype
## <character> <character> <character>
## AH91646 AHLRBaseDbs/v001/LRB.. https://github.com/r.. CSV
## AH91647 AHLRBaseDbs/v001/LRB.. https://github.com/r.. CSV
## AH91648 AHLRBaseDbs/v001/LRB.. https://github.com/r.. CSV
## AH91649 AHLRBaseDbs/v001/LRB.. https://github.com/r.. CSV
## AH91650 AHLRBaseDbs/v001/LRB.. https://github.com/r.. CSV
## ... ... ... ...
## AH111454 AHLRBaseDbs/v005/LRB.. https://github.com/r.. CSV
## AH111455 AHLRBaseDbs/v005/LRB.. https://github.com/r.. CSV
## AH111456 AHLRBaseDbs/v005/LRB.. https://github.com/r.. CSV
## AH111457 AHLRBaseDbs/v005/LRB.. https://github.com/r.. CSV
## AH111458 AHLRBaseDbs/v005/LRB.. https://github.com/r.. CSVWe can query only the LRBaseDb SQLite files for species Mus musculus.
qr <- query(ah, c("LRBaseDb", "Mus musculus"))
# filepath_mmu <- qr[[1]]This filepath is can be specified with the argument of RSQLite::dbConnect and
LRBaseDbi::LRBaseDb and also used as the argument of scTensor, which is an
R/Bioconductor package for the detection of cell-cell interaction detection.
For the details, check the vignettes of RSQLite, LRBaseDbi, and scTensor.
## R Under development (unstable) (2023-01-05 r83566)
## Platform: x86_64-apple-darwin21.6.0 (64-bit)
## Running under: macOS Monterey 12.6.2
##
## Matrix products: default
## BLAS: /Users/ka36530/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530/R-stuff/bin/R-devel/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: system (macOS)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnnotationHub_3.7.1 BiocFileCache_2.7.1 dbplyr_2.3.0
## [4] BiocGenerics_0.45.0 BiocStyle_2.27.1
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.39.0 xfun_0.37
## [3] bslib_0.4.2 Biobase_2.59.0
## [5] bitops_1.0-7 vctrs_0.5.2
## [7] tools_4.3.0 generics_0.1.3
## [9] stats4_4.3.0 curl_5.0.0
## [11] tibble_3.1.8 fansi_1.0.4
## [13] AnnotationDbi_1.61.0 RSQLite_2.2.20
## [15] blob_1.2.3 pkgconfig_2.0.3
## [17] S4Vectors_0.37.3 assertthat_0.2.1
## [19] GenomeInfoDbData_1.2.9 lifecycle_1.0.3
## [21] compiler_4.3.0 Biostrings_2.67.0
## [23] GenomeInfoDb_1.35.15 httpuv_1.6.9
## [25] htmltools_0.5.4 sass_0.4.5
## [27] RCurl_1.98-1.10 yaml_2.3.7
## [29] interactiveDisplayBase_1.37.0 pillar_1.8.1
## [31] later_1.3.0 crayon_1.5.2
## [33] jquerylib_0.1.4 ellipsis_0.3.2
## [35] cachem_1.0.6 mime_0.12
## [37] tidyselect_1.2.0 digest_0.6.31
## [39] purrr_1.0.1 dplyr_1.1.0
## [41] bookdown_0.32 BiocVersion_3.17.1
## [43] fastmap_1.1.0 cli_3.6.0
## [45] magrittr_2.0.3 utf8_1.2.3
## [47] withr_2.5.0 filelock_1.0.2
## [49] promises_1.2.0.1 rappdirs_0.3.3
## [51] bit64_4.0.5 rmarkdown_2.20
## [53] XVector_0.39.0 httr_1.4.4
## [55] bit_4.0.5 png_0.1-8
## [57] memoise_2.0.1 shiny_1.7.4
## [59] evaluate_0.20 knitr_1.42
## [61] IRanges_2.33.0 rlang_1.0.6
## [63] Rcpp_1.0.10 xtable_1.8-4
## [65] glue_1.6.2 DBI_1.1.3
## [67] BiocManager_1.30.19 jsonlite_1.8.4
## [69] R6_2.5.1 zlibbioc_1.45.0