This vignette shows how to find and download PTMsToPathways resources from ExperimentHub once the records are available.
library(ExperimentHub)
>> Loading required package: BiocGenerics
>> Loading required package: generics
>>
>> Attaching package: 'generics'
>> The following objects are masked from 'package:base':
>>
>> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
>> setequal, union
>>
>> Attaching package: 'BiocGenerics'
>> The following objects are masked from 'package:stats':
>>
>> IQR, mad, sd, var, xtabs
>> The following object is masked from 'package:utils':
>>
>> data
>> The following objects are masked from 'package:base':
>>
>> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>> get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
>> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
>> rbind, Reduce, rownames, sapply, saveRDS, scale, sequence, table,
>> tapply, transform, unique, unsplit, which.max, which.min
>> Loading required package: AnnotationHub
>> Loading required package: BiocFileCache
>> Loading required package: dbplyr
eh <- ExperimentHub()You can query directly:
Select an entry by index or by accession, then retrieve the object.
After a resource is downloaded once, ExperimentHub caches it locally and will reuse the cached copy in later sessions.
sessionInfo()
>> R version 4.6.1 (2026-06-24)
>> Platform: x86_64-pc-linux-gnu
>> Running under: Ubuntu 26.04.1 LTS
>>
>> Matrix products: default
>> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
>> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [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: Etc/UTC
>> tzcode source: system (glibc)
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] ExperimentHub_3.3.2 AnnotationHub_4.3.2 BiocFileCache_3.3.0
>> [4] dbplyr_2.6.0 BiocGenerics_0.59.12 generics_0.1.4
>> [7] rmarkdown_2.32
>>
>> loaded via a namespace (and not attached):
>> [1] rappdirs_0.3.4 sass_0.4.10 BiocVersion_3.24.0
>> [4] RSQLite_3.53.3 digest_0.6.39 magrittr_2.0.5
>> [7] evaluate_1.0.5 fastmap_1.2.0 blob_1.3.0
>> [10] jsonlite_2.0.0 AnnotationDbi_1.75.2 DBI_1.3.0
>> [13] BiocManager_1.30.27 httr_1.4.9 purrr_1.2.2
>> [16] Biostrings_2.81.9 httr2_1.3.0 jquerylib_0.1.4
>> [19] cli_3.6.6 crayon_1.5.3 rlang_1.3.0
>> [22] XVector_0.53.0 Biobase_2.73.2 bit64_4.8.6
>> [25] withr_3.0.3 cachem_1.1.0 yaml_2.3.12
>> [28] BiocBaseUtils_1.15.1 tools_4.6.1 memoise_2.0.1
>> [31] dplyr_1.2.1 filelock_1.0.3 curl_8.0.0
>> [34] png_0.1-9 buildtools_1.0.0 vctrs_0.7.3
>> [37] R6_2.6.1 stats4_4.6.1 lifecycle_1.0.5
>> [40] Seqinfo_1.3.2 KEGGREST_1.53.6 S4Vectors_0.51.10
>> [43] IRanges_2.47.5 bit_4.6.0 pkgconfig_2.0.3
>> [46] pillar_1.11.1 bslib_0.12.0 glue_1.8.1
>> [49] xfun_0.61 tibble_3.3.1 tidyselect_1.2.1
>> [52] sys_3.4.3 knitr_1.52 htmltools_0.5.9
>> [55] maketools_1.3.2 compiler_4.6.1