The AnVIL is cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utilities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programmatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to more formats more amenable to manipulation in R.
AnVIL 1.19.0
av*()
to work with AnVIL tables and data
avnotebooks*()
for notebook managementavworkflows_*()
for workflowsavworkspace_*()
for workspacesdrs_*()
for resolving DRS (Data Repository Service) URIsInstall the AnVIL package with
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager", repos = "https://cran.r-project.org")
BiocManager::install("AnVIL")
Once installed, load the package with
library(AnVILGCP)
library(AnVIL)
The AnVIL project is an analysis, visualization, and informatics cloud-based space for data access, sharing and computing across large genomic-related data sets.
The AnVIL project supports use of R through Jupyter notebooks and RStudio. Support for RStudio is preliminary as of April 2020.
This package provides access to AnVIL resources from within the AnVIL cloud, and also from stand-alone computing resources such as a user’s laptop.
Use of this package requires AnVIL and Google cloud computing billing accounts. Consult AnVIL training guides for details on establishing these accounts.
The remainder of this vignette assumes that an AnVIL account has been established and successfully linked to a Google cloud computing billing account.
In the AnVIL cloud environment, clone or create a new workspace. Click
on the Cloud Environment
button at the top right of the
screen. Choose the R / Bioconductor
runtime to use in a Jupyter
notebook, or RStudio
to use in RStudio. When creating a Jupyter
notebook, choose R
as the engine.
A new layout is being introduced in Fall of 2022. If the workspace has
an ‘Analyses’ tab, navigate to it and look for the ‘Environment
Configuration’ button to the right of the screen. For a Jupyter
notebook-based environment, select jupyter
‘Environment Settings’
followed by Customize
and the R / Bioconductor
application
configuration. RStudio is available by clicking on the RStudio / Bioconductor
‘Environment Settings’ button.
For tasks more complicated than manipulation and visualization of tabular data (e.g., performing steps of a single-cell work flow) the default Jupyter notebook configuration of 1 CPU and 3.75 GB of memory will be insufficient; the RStudio image defaults to 4 CPU and 15 GB of memory
Local use requires that the gcloud SDK is installed, and that the billing account used by AnVIL can be authenticated with the user. These requirements are satisfied when using the AnVIL compute cloud. For local use, one must
Install the gcloud sdk (for Linux and Windows,
cloudml::gcloud_install()
provides an alternative way to install
gcloud).
Define an environment variable or option()
named GCLOUD_SDK_PATH
pointing to the root of the SDK installation, e.g,
dir(file.path(Sys.getenv("GCLOUD_SDK_PATH"), "bin"), "^(gcloud|gsutil)$")
## [1] "gcloud" "gsutil"
Test the installation with gcloud_exists()
## the code chunks in this vignette are fully evaluated when
## gcloud_exists() returns TRUE
gcloud_exists()
## Warning in lifeCycle(newpackage = "AnVILGCP", package = "AnVIL", title = "gcloud"): 'gcloud_exists' is deprecated.
## Use 'AnVILGCP::gcloud_exists' instead.
## See help('gcloud-deprecated').
## [1] FALSE
Several commonly used functions have an additional ‘gadget’ interface,
allowing selection of workspaces (avworkspace_gadget()
, DATA tables
(avtable_gadget()
) and workflows avworkflow_gadget()
using a
simple tabular graphical user interface. The browse_workspace()
function allows selection of a workspace to be opened as a browser
tab.
The AnVIL cloud compute environment makes use of Docker containers
with defined installations of binary system software. Bioconductor
has arranged to build ‘binary’ R packages that work out of the
box with the BiocManager::install()
function. Binary packages
(when available and current) install without requiring compilation,
and are faster to install than packages built from source.
BiocManager::install("GenomicFeatures")
Thus BiocManager::install()
can be used as an improved method for
installing CRAN and Bioconductor binary and source packages.
Because package installation is fast, it can be convenient to install packages into libraries on a project-specific basis, e.g., to create a ‘snapshot’ of packages for reproducible analysis. Use
add_libpaths("~/my/project")
as a convenient way to prepend a project-specific library path to
.libPaths()
. New packages will be installed into this library.
The AnVIL package implements functions to facilitate access to Google cloud resources.
gcloud_*()
for account managementThe gcloud_*()
family of functions provide access to Google cloud
functions implemented by the gcloud
binary. gcloud_project()
returns the current billing account.
gcloud_account() # authentication account
gcloud_project() # billing project information
A convenient way to access any gcloud
SDK command is to use
gcloud_cmd()
, e.g.,
gcloud_cmd("projects", "list") %>%
readr::read_table() %>%
filter(startsWith(PROJECT_ID, "anvil"))
This translates into the command line gcloud projects list
. Help is
also available within R, e.g.,
gcloud_help("projects")
Use gcloud_help()
(with no arguments) for an overview of available
commands.
gsutil_*()
for file and bucket managementThe gsutil_*()
family of functions provides an interface to google
bucket manipulation. The following refers to publicly available 1000
genomes data available in Google Cloud Storage.
src <- "gs://genomics-public-data/1000-genomes/"
gsutil_ls()
lists bucket content; gsutil_stat()
additional detail
about fully-specified buckets.
gsutil_ls(src)
other <- paste0(src, "other")
gsutil_ls(other, recursive = TRUE)
sample_info <- paste0(src, "other/sample_info/sample_info.csv")
gsutil_stat(sample_info)
gsutil_cp()
copies buckets from or to Google cloud storage; copying
to cloud storage requires write permission, of course. One or both of
the arguments can be cloud endpoints.
fl <- tempfile()
gsutil_cp(sample_info, fl)
csv <- readr::read_csv(fl, guess_max = 5000L, col_types = readr::cols())
csv
gsutil_pipe()
provides a streaming interface that does not require
intermediate disk storage.
pipe <- gsutil_pipe(fl, "rb")
readr::read_csv(pipe, guess_max = 5000L, col_types = readr::cols()) %>%
dplyr::select("Sample", "Family_ID", "Population", "Gender")
gsutil_rsync()
synchronizes a local file hierarchy with a remote
bucket. This can be a powerful operation when delete = TRUE
(removing local or remote files), and has default option dry = TRUE
to indicate the consequences of the sync.
destination <- tempfile()
stopifnot(dir.create(destination))
source <- paste0(src, "other/sample_info")
## dry run
gsutil_rsync(source, destination)
gsutil_rsync(source, destination, dry = FALSE)
dir(destination, recursive = TRUE)
## nothing to synchronize
gsutil_rsync(source, destination, dry = FALSE)
## one file requires synchronization
unlink(file.path(destination, "README"))
gsutil_rsync(source, destination, dry = FALSE)
localize()
and delocalize()
provide ‘one-way’
synchronization. localize()
moves the content of the gs://
source
to the local file system. localize()
could be used at the
start of an analysis to retrieve data stored in the google cloud to
the local compute instance. delocalize()
performs the complementary
operation, copying local files to a gs://
destination. The unlink = TRUE
option to delocalize()
unlinks local source
files
recursively. It could be used at the end of an analysis to move
results to the cloud for long-term persistent storage.
av*()
to work with AnVIL tables and dataAnVIL organizes data and analysis environments into ‘workspaces’. AnVIL-provided data resources in a workspace are managed under the ‘DATA’ tab as ‘TABLES’, ‘REFERENCE DATA’, and ‘OTHER DATA’; the latter includes ‘’Workspace Data’ and ‘Files’, with ‘Files’ corresponding to a google cloud bucket associated with the workspace. These components of the graphical user interface are illustrated in the figure below.
The AnVIL package provides programmatic tools to access different components of the data workspace, as summarized in the following table.
Workspace | AnVIL function |
---|---|
TABLES | avtables() |
REFERENCE DATA | None |
OTHER DATA | avbucket() |
Workspace Data | avdata() |
Files | avfiles_ls() , avfiles_backup() , avfiles_restore() |
Data tables in a workspace are available by specifying the namespace
(billing account) and name
(workspace name) of the workspace. When
on the AnVIL in a Jupyter notebook or RStudio, this information can be
discovered with
avworkspace_namespace()
avworkspace_name()
It is also possible to specify, when not in the AnVIL compute environment, the data resource to work with.
## N.B.: IT MAY NOT BE NECESSARY TO SET THESE WHEN ON ANVIL
avworkspace_namespace("pathogen-genomic-surveillance")
avworkspace_name("COVID-19")
avtable*()
for accessing tablesAccessing data tables use the av*()
functions. Use avtables()
to
discover available tables, and avtable()
to retrieve a particular
table
avtables()
sample <- avtable("sample")
sample
The data in the table can then be manipulated using standard R commands, e.g., to identify SRA samples for which a final assembly fasta file is available.
sample %>%
select("sample_id", contains("fasta")) %>%
filter(!is.na(final_assembly_fasta))
Users can easily add tables to their own workspace using
avtable_import()
, perhaps as the final stage of a pipe
my_cars <-
mtcars |>
as_tibble(rownames = "model") |>
mutate(model = gsub(" ", "_", model))
job_status <- avtable_import(my_cars)
Tables are imported ‘asynchronously’, and large tables (more than 1.5
million elements; see the pageSize
argument) are uploaded in
pages. The job status
is a tibble summarizing each page; the status
of the upload can be checked with
avtable_import_status(job_status)
The transcript of a session where page size is set intentionally small for illustration is
(job_status <- avtable_import(my_cars, pageSize = 10))
## pageSize = 10 rows (4 pages)
## |======================================================================| 100%
## # A tibble: 4 × 5
## page from_row to_row job_id status
## <int> <int> <int> <chr> <chr>
## 1 1 1 10 a32e9706-f63c-49ed-9620-b214746b9392 Uploaded
## 2 2 11 20 f2910ac2-0954-4fb9-b36c-970845a266b7 Uploaded
## 3 3 21 30 e18adc5b-d26f-4a8a-a0d7-a232e17ac8d2 Uploaded
## 4 4 31 32 d14efb89-e2dd-4937-b80a-169520b5f563 Uploaded
(job_status <- avtable_import_status(job_status))
## checking status of 4 avtable import jobs
## |======================================================================| 100%
## # A tibble: 4 × 5
## page from_row to_row job_id status
## <int> <int> <int> <chr> <chr>
## 1 1 1 10 a32e9706-f63c-49ed-9620-b214746b9392 Done
## 2 2 11 20 f2910ac2-0954-4fb9-b36c-970845a266b7 Done
## 3 3 21 30 e18adc5b-d26f-4a8a-a0d7-a232e17ac8d2 ReadyForUpsert
## 4 4 31 32 d14efb89-e2dd-4937-b80a-169520b5f563 ReadyForUpsert
(job_status <- avtable_import_status(job_status))
## checking status of 4 avtable import jobs
## |======================================================================| 100%
## # A tibble: 4 × 5
## page from_row to_row job_id status
## <int> <int> <int> <chr> <chr>
## 1 1 1 10 a32e9706-f63c-49ed-9620-b214746b9392 Done
## 2 2 11 20 f2910ac2-0954-4fb9-b36c-970845a266b7 Done
## 3 3 21 30 e18adc5b-d26f-4a8a-a0d7-a232e17ac8d2 Done
## 4 4 31 32 d14efb89-e2dd-4937-b80a-169520b5f563 Done
The Terra data model allows for tables that represent samples of other
tables. The following create or add rows to participant_set
and
sample_set
tables. Each row represents a sample from the
corresponding ‘origin’ table.
## editable copy of '1000G-high-coverage-2019' workspace
avworkspace("anvil-datastorage/1000G-high-coverage-2019")
sample <-
avtable("sample") %>% # existing table
mutate(set = sample(head(LETTERS), nrow(.), TRUE)) # arbitrary groups
sample %>% # new 'participant_set' table
avtable_import_set("participant", "set", "participant")
sample %>% # new 'sample_set' table
avtable_import_set("sample", "set", "name")
The TABLES
data in a workspace are usually provided as curated
results from AnVIL. Nonetheless, it can sometimes be useful to delete
individual rows from a table. Use avtable_delete_values()
.
avdata()
for accessing Workspace DataThe ‘Workspace Data’ is accessible through avdata()
(the example
below shows that some additional parsing may be necessary).
avdata()
avbucket()
and workspace filesEach workspace is associated with a google bucket, with the content summarized in the ‘Files’ portion of the workspace. The location of the files is
bucket <- avbucket()
bucket
The content of the bucket can be viewed with
avfiles_ls()
If the workspace is owned by the user, then persistent data can be written to the bucket.
## requires workspace ownership
uri <- avbucket() # discover bucket
bucket <- file.path(uri, "mtcars.tab")
write.table(mtcars, gsutil_pipe(bucket, "w")) # write to bucket
A particularly convenient operation is to back up files or directories from the compute node to the bucket
## backup all files and folders in the current working directory
avfiles_backup(getwd(), recursive = TRUE)
## backup all files in the current directory
avfiles_backup(dir())
## backup all files to gs://<avbucket()>/scratch/
avfiles_backup(dir, paste0(avbucket(), "/scratch"))
Note that the backup operations have file naming behavior like the
Linux cp
command; details are described in the help page
gsutil_help("cp")
.
Use avfiles_restore()
to restore files or directories from the
workspace bucket to the compute node.
avnotebooks*()
for notebook managementPython (.ipynb
) or R (.Rmd
) notebooks are associated with
individual workspaces under the DATA tab, Files/notebooks
location.
Jupyter notebooks are exposed through the Terra interface under the NOTEBOOKS tab, and are automatically synchronized between the workspace and the current runtime.
R markdown documents may also be associated with the workspace (under
DATA Files/notebooks
) but are not automatically synchronized with
the current runtime. The functions in this section help manage R
markdown documents.
Available notebooks in the workspace are listed with
avnotebooks()
. Copies of the notebooks on the current runtime are
listed with avnotebooks(local = TRUE)
. The default location of the
notebooks is ~/<avworkspace_name()>/notebooks/
.
Use avnotebooks_localize()
to synchronize the version of the
notebooks in the workspace to the current runtime. This operation
might be used when a new runtime is created, and one wishes to start
with the notebooks found in the workspace. If a newer version of the
notebook exists in the workspace, this will overwrite the older
version on the runtime, potentially causing data loss. For this
reason, avnotebooks_localize()
by default reports the actions that
will be performed, without actually performing them. Use
avnotebooks_localize(dry = FALSE)
to perform the localization.
Use avnotebooks_delocalize()
to synchronize local versions of the
notebooks on the current runtime to the workspace. This operation
might be used when developing a workspace, and wishing to update the
definitive notebook in the workspace. When dry = FALSE
, this
operation also overwrites older workspace notebook files with their
runtime version.
avworkflows_*()
for workflowsSee the vignette “Running an AnVIL workflow within R”, in this package, for details on running workflows and managing output.
avworkspace_*()
for workspacesavworkspace()
is used to define or return the ‘namespace’ (billing
project) and ‘name’ of the workspace on which operations are to
act. avworkspace_namespace()
and avworkspace_name()
can be used to
set individual elements of the workspace.
avworkspace_clone()
clones a workspace to a new location. The clone
includes the ‘DATA’, ‘NOTEBOOK’, and ‘WORKFLOWS’ elements of the
workspace.
drs_*()
for resolving DRS (Data Repository Service) URIsThe Data Repository Service (DRS) is a GA4GH standard that separates a
resource location (e.g., google bucket of a VCF file) from the URI
that identifies the resource. A URI with the form drs://...
is submitted to the Terra / AnVIL DRS, and translated to bucket (e.g., gs://...
) or
https://...
URIs. One use case for DRS is when the location (e.g.,
google bucket) of the resouce moves. In this case the DRS identifier
does not change, so no changes are needed to code or data resources
that referenced the object. A second use case is when access to a
resource is restricted. The DRS URI in conjunction with appropriate
credentials can then be translated to a ‘signed’ https URL that
encodes authentication information, allowing standard software like a
web browser, or R commands like download.file()
or
VariantAnnotation::readVcf()
to access the resource. A Terra support
article provides more information, though not about DRS in R!
The following DRS URIs identify a 1000 Genomes VCF file and it’s index
uri <- c(
vcf = "drs://dg.ANV0/6f633518-f2de-4460-aaa4-a27ee6138ab5",
tbi = "drs://dg.ANV0/4fb9e77f-c92a-4deb-ac90-db007dc633aa"
)
Information about the URIs can be discovered with drs_stat()
tbl <- drs_stat(uri)
## # A tibble: 2 × 9
## drs fileName size gsUri accessUrl timeUpdated hashes bucket name
## <chr> <chr> <dbl> <chr> <chr> <chr> <list> <chr> <chr>
## 1 drs://d… NA21144… 7.06e9 gs:/… NA 2020-07-08… <named list> fc-56… CCDG…
## 2 drs://d… NA21144… 4.08e6 gs:/… NA 2020-07-08… <named list> fc-56… CCDG…
Column names indicate the information that is avaialable, e.g., the
google object (gsUri
) and size (size
) of the object, and the
object’s file name (fileName
)
drs_cp()
provides a convient way to translate DRS URIs to gs://
URIs, and to copy files from their cloud location to the local disk or
another bucket, e.g.,
drs_cp(uri, "/tmp") # local temporary directory
drs_cp(uri, avbucket()) # workspace bucket
drs_access_url()
translates the DRS URI to a standard HTTPS URI, but
with additional authentication information embedded. These HTTPS URIs
are usually time-limited. They can be used like regular HTTPS URIs, e.g,
suppressPackageStartupMessages({
library(VariantAnnotation)
})
https <- drs_access_url(uri)
vcffile <- VcfFile(https[["vcf"]], https[["tbi"]])
scanVcfHeader(vcffile)
## class: VCFHeader
## samples(1): NA21144
## meta(3): fileformat reference contig
## fixed(2): FILTER ALT
## info(16): BaseQRankSum ClippingRankSum ... ReadPosRankSum VariantType
## geno(11): GT AB ... PL SB
variants <- readVcf(vcffile, param = GRanges("chr1:1-1000000"))
nrow(variants)
## [1] 123077
The buckets are both ‘requester pays’ (see
gsutil_requesterpays(uri)
), so these queries are billed to the
current project.
AnVIL applications are exposed to the developer through RESTful API
services. Each service is represented in R as an object. The object
is created by invoking a constructor, sometimes with arguments. We
illustrate basic functionality with the Terra()
service.
Currently, APIs using the OpenAPI Specification (OAS) Version 2 (formerly known as Swagger) are supported. AnVIL makes use of the rapiclient codebase to provide a unified representation of the API protocol.
Create an instance of the service. This consults a Swagger / OpenAPI schema corresponding to the service to create an object that knows about available endpoints. Terra / AnVIL project services usually have Swagger / OpenApi-generated documentation, e.g., for the Terra service.
terra <- Terra()
Printing the return object displays a brief summary of endpoints
terra
The schema for the service groups endpoints based on tag values,
providing some level of organization when exploring the service. Tags
display consists of endpoints (available as a tibble with
tags(terra)
).
terra %>% tags("Status")
Access an endpoint with $
; without parentheses ()
this generates a
brief documentation string (derived from the schema
specification. Including parentheses (and necessary arguments) invokes
the endpoint.
terra$status
terra$status()
Some arguments appear in the ‘body’ of a REST request. Provide these
as a list specified with .__body__ = list(...)
; use args()
to
discover whether arguments should be present in the body of the
request. For instance,
args(terra$createBillingProjectFull)
shows that all arguments should be included in the .__body__=
argument. A more complicated example is
args(terra$overwriteWorkspaceMethodConfig)
where the same argument name appears in both the URL and the
body. Again, the specification of the body arguments should be in
.__body__ = list()
. As a convenience, arguments appearing only in
the body can also be specified in the ...
argument of the reqeust.
operations()
and schemas()
return a named list of endpoints, and
of argument and return value schemas. operations(terra)$XXX()
can be
used an alternative to direct invocation terra$XXX()
. schemas()
can be used to construct function arguments with complex structure.
empty_object()
is a convenience function to construct an ‘empty’
object (named list without content) required by some endpoints.
Endpoints return objects of class response
, defined in the httr package
status <- terra$status()
class(status)
Several convenience functions are available to help developers transform return values into representations that are more directly useful.
str()
is invoked for the side-effect of displaying the list-like
structure of the response. Note that this is not the literal structure
of the response
object (use utils::str(status)
for that), but
rather the structure of the JSON response received from the service.
str(status)
as.list()
returns the JSON response as a list, and flatten()
attempts to transform the list into a tibble. flatten()
is effective
when the response is in fact a JSON row-wise representation of
tibble-like data.
lst <- status %>% as.list()
lengths(lst)
lengths(lst$systems)
str(lst$systems)
Testing endpoints is challenging. Endpoints cannot be evaluated directly because they required credentialed access, and because remote calls involve considerable latency and sometimes bandwidth. Traditional ‘mocks’ are difficult to implement because of the auto-generated nature of endpoints from APIs. Simply checking for identical API YAML files (e.g., using md5sums) only indicates a change in the file without assessing whether the R code invoking the endpoint is the same (e.g., because arguments were added, removed, or renamed).
The approach adopted here is to take a ‘snapshot’ of the current API. This is then compared to the updated API. Endpoints that are used in the code but that have been removed or have updated arguments are then manually checked for conformance to the updated API. Once endpoints are brought into line with the new API, the snapshot is updated to reflect the new API.
Non-exported functions in the AnVIL package facilitate these steps. For
instance, AnVIL:::.api_test_write(Terra(), "Terra")
creates a
snapshot of the current API. This is saved as
tests/testthat/api-Terra.rds
. The service is then updated (following
the README of inst/services/terra
) and the updated API compared to
the original with AnVIL::.api_test_check(Terra(), "Terra")
. The
result is a list of functions that are common to both APIs, or added,
removed, or updated (different arguments) in the new API. A static
example is
> .api_test_check(Terra(), "Terra") |> lengths()
common added removed updated common_in_use
135 24 3 11 9
removed_in_use updated_in_use
0 3
with the removed_in_use
and updated_in_use
endpoints
> .api_test_check(Terra(), "Terra")[c("removed_in_use", "updated_in_use")]
$removed_in_use
character(0)
$updated_in_use
[1] "cloneWorkspace" "entityQuery" "flexibleImportEntities"
requiring manual inspection. Manual inspection means that each use in
the AnVIL R package code is examined and updated to match the new
API. Once the R code is aligned with the new API, .api_test_write()
is re-run. The commit consists of the updated API files in
inst/services
, updated R code, and the updated snapshot.
Unit tests (in test_api.R
) are implemented to fail when the
removed_in_use
or updated_in_use
fields are not zero-length.
The AnVIL package implements and has made extensive use of the following services:
Terra()
) provides access to
terra account and workspace management, and is meant as the primary
user-facing ‘orchestration’ API.Leonardo (https://leonardo.dev.anvilproject.org/; Leonardo()
)
implements an interface to the AnVIL container deployment service,
useful for management Jupyter notebook and RStudio sessions running
in the AnVIL compute cloud.
Rawls (https://rawls.dsde-prod.broadinstitute.org; Rawls()
)
implements functionality that often overlaps with (and is delegated
to) the Terra interface; the Rawls interface implements
lower-level functionality, and some operations (e.g., populating a
DATA TABLE) are more difficult to accomplish with Rawls.
The Dockstore service (https://dockstore.org/swagger.json,
Dockstore()
) is available but has received limited
testing. Dockstore is used to run CWL- or WDL-based work flows,
including workflows using R / Bioconductor. See the separate
vignette ‘Dockstore and Bioconductor for AnVIL’ for initial
documentation.
Service
class to implement your own RESTful interfaceThe AnVIL package provides useful functionality for exposing other RESTful services represented in Swagger. To use this in other packages,
Add to the package DESCRIPTION file
Imports: AnVIL
Arrange (e.g., via roxygen2 @importFrom
, etc.) for the NAMESPACE
file to contain
importFrom AnVIL, Service
importMethodsFrom AnVIL, "$" # pehaps also `tags()`, etc
importClassesFrom AnVIL, Service
Implement your own class definition and constructor. Use ?Service
to provide guidance on argument specification. For instance, to
re-implement the terra service.
.MyService <- setClass("MyService", contains = "Service")
MyService <-
function()
{
.MyService(Service(
"myservice",
host = "api.firecloud.org",
api_url = "https://api.firecloud.org/api-docs.yaml",
authenticate = FALSE
))
}
Use api_reference_url
and api_reference_md5sum
of Service()
as a
mechanism to provide some confidence that the service created by the
user at runtime is consistent with the service intended by the
developer.
For user support, please ask for help on the Bioconductor support site. Remember to tag your question with ‘AnVIL’, so that the maintainer is notified. Ask for developer support on the bioc-devel mailing list.
Please report bugs as ‘issues’ on GitHub.
Retrieve the source code for this package from it’s canonical location.
git clone https://git.bioconductor.org/packages/AnVIL
The package source code is also available on GitHub
Research reported in this software package was supported by the US National Human Genomics Research Institute of the National Institutes of Health under award number U24HG010263. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.