AHLRBaseDbs 1.5.0
Authors: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Last modified: 2022-10-19 10:01:27
Compiled: Wed Oct 19 10:01:40 2022
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 501 records
## # snapshotDate(): 2022-10-18
## # $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)
## ... ...
## AH107263 | LRBaseDb for Taeniopygia guttata (Zebra finch, v004)
## AH107264 | LRBaseDb for Takifugu rubripes (Fugu, v004)
## AH107265 | LRBaseDb for Ursus maritimus (Polar bear, v004)
## AH107266 | LRBaseDb for Vulpes vulpes (Red fox, v004)
## AH107267 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v004)We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket
with mcols().
mcols(query(ah, "LRBaseDb"))## DataFrame with 501 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
## ... ... ... ...
## AH107263 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,.. Taeniopygia guttata
## AH107264 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,.. Takifugu rubripes
## AH107265 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,.. Ursus maritimus
## AH107266 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,.. Vulpes vulpes
## AH107267 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
## ... ... ... ... ...
## AH107263 59729 NA Correspondence table.. 1
## AH107264 31033 NA Correspondence table.. 1
## AH107265 29073 NA Correspondence table.. 1
## AH107266 9627 NA Correspondence table.. 1
## AH107267 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
## ... ... ... ...
## AH107263 Koki Tsuyuzaki <k.t... 2022-09-30 AHLRBaseDbs
## AH107264 Koki Tsuyuzaki <k.t... 2022-09-30 AHLRBaseDbs
## AH107265 Koki Tsuyuzaki <k.t... 2022-09-30 AHLRBaseDbs
## AH107266 Koki Tsuyuzaki <k.t... 2022-09-30 AHLRBaseDbs
## AH107267 Koki Tsuyuzaki <k.t... 2022-09-30 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
## ... ... ...
## AH107263 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH107264 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH107265 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH107266 Annotation,BADERLAB,BIOMART,... SQLiteFile
## AH107267 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
## ... ... ... ...
## AH107263 AHLRBaseDbs/v004/LRB.. https://github.com/r.. CSV
## AH107264 AHLRBaseDbs/v004/LRB.. https://github.com/r.. CSV
## AH107265 AHLRBaseDbs/v004/LRB.. https://github.com/r.. CSV
## AH107266 AHLRBaseDbs/v004/LRB.. https://github.com/r.. CSV
## AH107267 AHLRBaseDbs/v004/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 4.2.0 Patched (2022-05-05 r82321)
## Platform: x86_64-apple-darwin19.6.0 (64-bit)
## Running under: macOS Catalina 10.15.7
##
## Matrix products: default
## BLAS: /Users/ka36530_ca/R-stuff/bin/R-4-2/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-2/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnnotationHub_3.5.2 BiocFileCache_2.5.0 dbplyr_2.2.1
## [4] BiocGenerics_0.43.4 BiocStyle_2.25.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 png_0.1-7
## [3] Biostrings_2.65.6 assertthat_0.2.1
## [5] digest_0.6.29 utf8_1.2.2
## [7] mime_0.12 R6_2.5.1
## [9] GenomeInfoDb_1.33.7 stats4_4.2.0
## [11] RSQLite_2.2.17 evaluate_0.16
## [13] httr_1.4.4 pillar_1.8.1
## [15] zlibbioc_1.43.0 rlang_1.0.6
## [17] curl_4.3.3 jquerylib_0.1.4
## [19] blob_1.2.3 S4Vectors_0.35.4
## [21] rmarkdown_2.16 stringr_1.4.1
## [23] RCurl_1.98-1.8 bit_4.0.4
## [25] shiny_1.7.2 compiler_4.2.0
## [27] httpuv_1.6.6 xfun_0.33
## [29] pkgconfig_2.0.3 htmltools_0.5.3
## [31] tidyselect_1.2.0 KEGGREST_1.37.3
## [33] GenomeInfoDbData_1.2.9 tibble_3.1.8
## [35] interactiveDisplayBase_1.35.0 bookdown_0.29
## [37] IRanges_2.31.2 fansi_1.0.3
## [39] withr_2.5.0 crayon_1.5.2
## [41] dplyr_1.0.10 later_1.3.0
## [43] bitops_1.0-7 rappdirs_0.3.3
## [45] jsonlite_1.8.2 xtable_1.8-4
## [47] lifecycle_1.0.3 DBI_1.1.3
## [49] magrittr_2.0.3 cli_3.4.1
## [51] stringi_1.7.8 cachem_1.0.6
## [53] XVector_0.37.1 promises_1.2.0.1
## [55] bslib_0.4.0 ellipsis_0.3.2
## [57] filelock_1.0.2 generics_0.1.3
## [59] vctrs_0.4.2 tools_4.2.0
## [61] bit64_4.0.5 Biobase_2.57.1
## [63] glue_1.6.2 purrr_0.3.5
## [65] BiocVersion_3.16.0 fastmap_1.1.0
## [67] yaml_2.3.5 AnnotationDbi_1.59.1
## [69] BiocManager_1.30.18 memoise_2.0.1
## [71] knitr_1.40 sass_0.4.2