Package: HTAN 0.99.1

Sean Davis

HTAN: Query and Retrieve Human Tumor Atlas Network (HTAN) Open-Access Data

A client for the open-access data of the Human Tumor Atlas Network (HTAN), Phase 1. File, biospecimen, clinical and provenance metadata are queried locally from a versioned parquet snapshot of the ISB-CGC HTAN BigQuery release tables, through DuckDB and dbplyr, with no Google account. Open-access files are downloaded from the CRDC General Commons (anonymous GA4GH DRS) or Synapse (personal access token), and common HTAN file formats are read into Bioconductor classes such as SingleCellExperiment, SpatialExperiment and MultiAssayExperiment.

Authors:Sean Davis [aut, cre], National Cancer Institute [fnd]

HTAN_0.99.1.tar.gz
HTAN_0.99.1.zip(r-4.7-any)HTAN_0.99.1.zip(r-4.6-any)HTAN_0.99.1.zip(r-4.5-any)
HTAN_0.99.1.tgz(r-4.6-any)HTAN_0.99.1.tgz(r-4.5-any)
HTAN_0.99.1.tar.gz(r-4.7-any)HTAN_0.99.1.tar.gz(r-4.6-any)
HTAN_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HTAN/json (API)

# Install 'HTAN' in R:
install.packages('HTAN', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/seandavi/htan/issues

Pkgdown/docs site:https://seandavi.github.io

On CRAN:

Conda:

dataimportdatarepresentationbiomedicalinformaticssinglecellspatialthirdpartyclienttranscriptomicsquarto

3.60 score 8 scripts 11 exports 61 dependencies

Last updated from:9efae6be0a. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE329
linux-develOK244
source / vignettesOK525
linux-releaseOK397
macos-releaseOK213
macos-oldrelOK148
windows-develOK235
windows-releaseOK456
windows-oldrelOK206
wasm-releaseOK327

Exports:htan_columnshtan_conhtan_disconnecthtan_downloadhtan_experimenthtan_fileshtan_lineagehtan_snapshot_infohtan_tableshtan_tblread_htan

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyrduckdbfastmapfilelockgenericsGenomicRangesgluehttr2IRangesjsonlitelatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseMultiAssayExperimentopensslpillarpkgconfigpurrrR6RcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector

Exploring the HTAN Phase 1 atlas
Building the working tables | The release at a glance | Centers | Organs and cancer types | Assays and data levels | Which assays, at which levels | Who ran what | Multiplexed imaging technologies | Single-cell and spatial coverage | What is ready to analyse | Biospecimens | Clinical variables | What is recorded | How complete it is | Demographics and outcome | Time: longitudinal sampling | Summary | Session information
Rendered fromatlas-overview.qmdusingquarto::html

Last update: 2026-10-20
Started: 2026-10-14

The HTAN data model, identifiers and lineage
The data model in brief | Clinical data | The main tables | File components | Identifiers | The grammar | Do not parse the participant out of a file ID | The hierarchy: participant, biospecimen, file | Biospecimens | Files | id_provenance, the lineage table | Worked lineage walks | A Visium spatial transcriptomics object, back to the patient | Comma-separated parents | Descendants of a raw file | A multiplexed imaging cell table | A file from several participants | Pitfalls | Summary | Session information
Rendered fromdata-model.qmdusingquarto::html

Last update: 2026-10-20
Started: 2026-10-14

From query to analysis
Choosing a dataset | The question | Finding candidate files | What the metadata say about it | Tracing lineage | Downloading | Reading into a SpatialExperiment | Adding clinical context: a MultiAssayExperiment | Analysis | Quality control | Normalisation | Feature selection and dimensionality reduction | Clustering | What the clusters are | Where to go from here | Notes on reproducibility | Session information
Rendered fromanalysis-workflow.qmdusingquarto::html

Last update: 2026-10-20
Started: 2026-10-14

Introduction to HTAN
Introduction | Installation | Getting started | What HTAN is | Phase 1 | Phase 2 | How HTAN data are organised | Participants, biospecimens and files | Data levels | Access tiers | Where the data live, and why | What this package does, and what it doesn't | The metadata snapshot | What it is | How it relates to the authoritative sources | A quick tour | Tables and columns | Files | Lineage | Downloading files | Reading and assembling | How these vignettes are built | References | Session information
Rendered fromHTAN.qmdusingquarto::html

Last update: 2026-10-20
Started: 2026-10-14