HPAStainR
1.12.0BioconductorQueries the Human Protein Atlas Staining Data for Multiple Proteins and Genes
No longer in Bioconductor
- Last in
- Bioconductor 3.18, 25 Oct 2023
- First without it
- 3.19, 1 May 2024
- Bioconductor build, method
Method
Checks and health
CRAN runs every current package through R CMD check on a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.
- Problems
- Notes alone never count against a package, but a warning, an error or a failure on any platform is a problem. Open CRAN deadlines are a fact of their own, shown as a clock after the mark, so the mark always says what the checks found.
- Checks only
- Health reflects CRAN's check results and nothing else. Even a package with no tests, no coverage or no recent release can have every platform OK.
- Once a day
- Results are collected once a day from files CRAN publishes. Each platform is one machine set-up, named by its R version, operating system, architecture and compiler, such as r-devel-linux-x86_64-fedora-clang.
- Platforms counted
- The 13 in 3 of 13 is the number of platform rows CRAN published for that package on the day of collection. The set of machines changes over time, so the number is not fixed, and a package missing from a platform counts as neither passing nor failing there.
- No reportnone on record
- Distinct IPs a month, method
- 83Rank 3,011 in its category
- Dependent packages, method
Method
Reverse dependencies
Dependent packages are other packages that list this one under Depends, Imports or LinkingTo in their DESCRIPTION file. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.
- As declared
- The counts follow the declarations as written, not whether a package uses the other one when it runs.
- Suggests apart
- Packages that list this one only under Suggests install and run without it, and use it for tests, examples or an optional feature. They are counted as Suggested by, never among the dependents, and a package that also lists it under one of the three fields is a dependent and is not counted again.
- Zero
- Zero dependents means no current CRAN package declares a need for this one, though some may suggest it. On 26 Oct 2026, 19,530 of the 25,531 current CRAN packages had no dependent package.
- 0none suggest it
- Bioconductor releases
- 7since 2020
- Advisories, method
Method
Security advisories
Advisories come from the R Consortium advisory database, a community record of security problems in R packages, as OSV publishes it.
- The copy
- The record is read once a day. The data is published under the Apache License 2.0 and is credited on the advisories list.
- Box under the name
- Under the package's name, a box names any advisory that affects the current release, with its fix or that there is none.
- Ranges
- Advisories state ranges, such as from 0.9.12 up to but not including 1.8.8. Each range is checked against every version CRAN has published, using the version rules R itself uses, so a release that came out after the advisory was written is still caught by its range.
- Not the package
- The rating is for the library flaw itself, not for how exposed the R package is, and it is never added up into a figure for the package.
- None publishedfor Bioconductor
About
Method, About Method Licence figures come from the License field of each package's DESCRIPTION file, read the way R itself reads it. No licence file is opened.Licences
This package is built around the HPAStainR function. The purpose of the HPAStainR function is to query the visual staining data in the Human Protein Atlas to return a table of staining ranked cell types.
Full description
This package is built around the HPAStainR function. The purpose of the HPAStainR function is to query the visual staining data in the Human Protein Atlas to return a table of staining ranked cell types. The function also has multiple arguments to personalize to output as well to include cancer data, csv readable names, modify the confidence levels of the results and more. The other functions exist exclusively to easily acquire the data required to run HPAStainR.
- Licence
- Artistic-2.0
- First release
- Bioconductor 3.12, 28 Oct 2020
More details
- Releases
- 7 of 49 Bioconductor releases
- Needs R
- >= 4.1.0
biocViews (2)
Cite
Package
Run in R for the authors' preferred citation:
citation("HPAStainR")Nieuwenhuis, T. O. (2023). HPAStainR: Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes (Version 1.12.0) [Computer software]. https://bioconductor.org/packages/HPAStainR
About
This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
Balamuta, J. J. (2026). R Observatory: Metrics for HPAStainR version 1.12.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040
About
From data release v2026-10-26, which the citation names so these numbers can be found later.
Health
No build report is on record for this package.
Downloads
Method, Downloads Method Download figures count requests logged by each distribution channel. They are not counts of installs or of users, because each channel publishes its own totals and this site reads them.Downloads
- Total downloads in the latest complete month
- 525It comes from Bioconductor alone. Bioconda was counted over another window, so it is not added.
Rank in category, by distinct IPs
3,011 of 3,170
Bioconductor
525 downloads in the latest complete month
Distinct IP addresses average 83 a month over 12 months, which is a different measure and is never added.
It is in the total. Take it out
Bioconda
31 downloads in the last 30 days
It is not added because it has no figure for the latest complete month.
The total is 525 downloads in the latest complete month. It comes from Bioconductor alone.
This local copy has no series over time.
Dependencies
Code
Method, Code Method Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.Code metrics
The code of this package has not been analysed.
People
Method, People Method People on the site are the names packages give them in their DESCRIPTION files: authors from the author list, and the maintainer from the Maintainer field. Spellings of one name become one person only where the rules below allow it, and when in doubt the rules keep people apart.Author and maintainer identity
Repository
Method, figures by host Method Repository signals are the figures read from the source repository a package links to: stars, forks, issues, commits, releases and the time issues take to close. They are read from GitHub, GitLab and Codeberg.Repository signals
No repository on record
History
Method, History Method Archived is built from CRAN's archive records, its list of check deadlines and Bioconductor's package records. Every figure is counted to 26 Oct 2026, the day the data was read.Packages leaving
- In Bioconductor
- In no release
- Bioconductor release
| Release | Released | R |
|---|---|---|
| 3.18 | 25 Oct 2023 | 4.3 |
| 3.17 | 26 Apr 2023 | 4.3 |
| 3.16 | 2 Nov 2022 | 4.2 |
| 3.15 | 27 Apr 2022 | 4.2 |
| 3.14 | 27 Oct 2021 | 4.1 |
| 3.13 | 20 May 2021 | 4.1 |
| 3.12 | 28 Oct 2020 | 4.0 |
- Entered Bioconductor
- Release 3.12, 28 Oct 2020