AHLRBaseDbs 1.7.0
Authors: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Last modified: 2023-10-17 09:41:25.611888
Compiled: Tue Oct 17 09:44:31 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 749 records
## # snapshotDate(): 2023-10-05
## # $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)
## ... ...
## AH113975 | LRBaseDb for Taeniopygia guttata (Zebra finch, v006)
## AH113976 | LRBaseDb for Takifugu rubripes (Fugu, v006)
## AH113977 | LRBaseDb for Ursus maritimus (Polar bear, v006)
## AH113978 | LRBaseDb for Vulpes vulpes (Red fox, v006)
## AH113979 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v006)We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket
with mcols().
mcols(query(ah, "LRBaseDb"))## DataFrame with 749 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
## ... ... ... ...
## AH113975 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,.. Taeniopygia guttata
## AH113976 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,.. Takifugu rubripes
## AH113977 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,.. Ursus maritimus
## AH113978 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,.. Vulpes vulpes
## AH113979 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
## ... ... ... ... ...
## AH113975 59729 NA Correspondence table.. 1
## AH113976 31033 NA Correspondence table.. 1
## AH113977 29073 NA Correspondence table.. 1
## AH113978 9627 NA Correspondence table.. 1
## AH113979 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
## ... ... ... ...
## AH113975 Koki Tsuyuzaki <k.t... 2023-09-27 AHLRBaseDbs
## AH113976 Koki Tsuyuzaki <k.t... 2023-09-27 AHLRBaseDbs
## AH113977 Koki Tsuyuzaki <k.t... 2023-09-27 AHLRBaseDbs
## AH113978 Koki Tsuyuzaki <k.t... 2023-09-27 AHLRBaseDbs
## AH113979 Koki Tsuyuzaki <k.t... 2023-09-27 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
## ... ... ...
## AH113975 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH113976 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH113977 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH113978 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH113979 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
## ... ... ... ...
## AH113975 AHLRBaseDbs/v006/LRB.. https://github.com/r.. CSV
## AH113976 AHLRBaseDbs/v006/LRB.. https://github.com/r.. CSV
## AH113977 AHLRBaseDbs/v006/LRB.. https://github.com/r.. CSV
## AH113978 AHLRBaseDbs/v006/LRB.. https://github.com/r.. CSV
## AH113979 AHLRBaseDbs/v006/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 version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnnotationHub_3.9.2 BiocFileCache_2.9.1 dbplyr_2.3.4
## [4] BiocGenerics_0.47.0 BiocStyle_2.29.2
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.41.4 xfun_0.40
## [3] bslib_0.5.1 Biobase_2.61.0
## [5] bitops_1.0-7 vctrs_0.6.4
## [7] tools_4.3.1 generics_0.1.3
## [9] stats4_4.3.1 curl_5.1.0
## [11] tibble_3.2.1 fansi_1.0.5
## [13] AnnotationDbi_1.63.2 RSQLite_2.3.1
## [15] blob_1.2.4 pkgconfig_2.0.3
## [17] S4Vectors_0.39.3 GenomeInfoDbData_1.2.10
## [19] lifecycle_1.0.3 compiler_4.3.1
## [21] Biostrings_2.69.2 GenomeInfoDb_1.37.6
## [23] httpuv_1.6.11 htmltools_0.5.6.1
## [25] sass_0.4.7 RCurl_1.98-1.12
## [27] yaml_2.3.7 interactiveDisplayBase_1.39.0
## [29] pillar_1.9.0 later_1.3.1
## [31] crayon_1.5.2 jquerylib_0.1.4
## [33] ellipsis_0.3.2 cachem_1.0.8
## [35] mime_0.12 tidyselect_1.2.0
## [37] digest_0.6.33 purrr_1.0.2
## [39] dplyr_1.1.3 bookdown_0.35
## [41] BiocVersion_3.18.0 fastmap_1.1.1
## [43] cli_3.6.1 magrittr_2.0.3
## [45] utf8_1.2.3 withr_2.5.1
## [47] filelock_1.0.2 promises_1.2.1
## [49] rappdirs_0.3.3 bit64_4.0.5
## [51] rmarkdown_2.25 XVector_0.41.1
## [53] httr_1.4.7 bit_4.0.5
## [55] png_0.1-8 memoise_2.0.1
## [57] shiny_1.7.5.1 evaluate_0.22
## [59] knitr_1.44 IRanges_2.35.3
## [61] rlang_1.1.1 Rcpp_1.0.11
## [63] xtable_1.8-4 glue_1.6.2
## [65] DBI_1.1.3 BiocManager_1.30.22
## [67] jsonlite_1.8.7 R6_2.5.1
## [69] zlibbioc_1.47.0