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AssessORFData

Bioc current

Data and Files for the AssessORF Package

v1.30.0 · Package record · experiment · GPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.8 · Oct 31, 2018

Current · Requires R 4.6

1.0 In 16 of 49 releases 3.23

Description

This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

5 5 exported

Complexity

5.2 avg / 10 max

Call network

5 nodes / 4 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

5,559

Files

175

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,737 (49.2%)Docs 2,748 (49.4%)Vignettes 74 (1.3%)

API

Exported functions

5

Internal functions

0

Recent export changes

v3.8+5 GetDataMapObj, GetGeneSources, GetResultsObj +2 more

Testing

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

33.3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

16

First release

2018-10-30

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

1

LOC over versions

v3.8: 4,355 LOCv3.9: 4,355 LOCv3.10: 5,559 LOCv3.11: 5,559 LOCv3.12: 5,559 LOCv3.13: 5,559 LOCv3.14: 5,559 LOCv3.15: 5,559 LOCv3.16: 5,559 LOCv3.17: 5,559 LOCv3.18: 5,559 LOCv3.19: 5,559 LOCv3.20: 5,559 LOCv3.21: 5,559 LOCv3.22: 5,559 LOCv3.23: 5,559 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

In the Bioconductor 3.23 release
READMEYes · 2 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION
Help pages
32
Examples that run
100%5 run in a plain check
Exported functions with examples
100%
Documented parameters
100%
Return-value docs
100%
Help pages citing references
0%
Vignettes (1)
How these are measured

Repository practices

Bioconductor git repository

Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.

No development-tooling practices detected in the Bioconductor git repository.

How this is detected

Datasets

Bundled datasets · 131
NameClassSizeAlso in
AP1_PreSaved_DataMapObjAssessment16 elementsNo other package
AP1_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
AP1_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
AP1_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
AP1_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
ATCC11842_PreSaved_DataMapObjAssessment16 elementsNo other package
ATCC11842_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
ATCC11842_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
ATCC11842_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
ATCC11842_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
ATCC13032_PreSaved_DataMapObjAssessment16 elementsNo other package
ATCC13032_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
ATCC13032_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
ATCC13032_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
ATCC13032_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
ATCC17978_PreSaved_DataMapObjAssessment16 elementsNo other package
ATCC17978_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
ATCC17978_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
ATCC17978_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
ATCC17978_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
ATCC700084_PreSaved_DataMapObjAssessment16 elementsNo other package
ATCC700084_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
ATCC700084_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
ATCC700084_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
ATCC700084_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
AssessORF_StrainIDsvector26 elementsNo other package
BW25113_PreSaved_DataMapObjAssessment16 elementsNo other package
BW25113_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
BW25113_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
BW25113_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
BW25113_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
CCMP1375_PreSaved_DataMapObjAssessment16 elementsNo other package
CCMP1375_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
CCMP1375_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
CCMP1375_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
CCMP1375_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
CECT5344_PreSaved_DataMapObjAssessment16 elementsNo other package
CECT5344_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
CECT5344_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
CECT5344_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
CECT5344_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
CNRZ327_PreSaved_DataMapObjAssessment16 elementsNo other package
CNRZ327_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
CNRZ327_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
CNRZ327_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
CNRZ327_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
COH1_PreSaved_DataMapObjAssessment16 elementsNo other package
COH1_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
COH1_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
COH1_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
COH1_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
D_UW_3_CX_PreSaved_DataMapObjAssessment16 elementsNo other package
D_UW_3_CX_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
D_UW_3_CX_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
D_UW_3_CX_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
D_UW_3_CX_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
EGD_e_PreSaved_DataMapObjAssessment16 elementsNo other package
EGD_e_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
EGD_e_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
EGD_e_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
EGD_e_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
H37Rv_PreSaved_DataMapObjAssessment16 elementsNo other package
H37Rv_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
H37Rv_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
H37Rv_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
H37Rv_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
HG001_PreSaved_DataMapObjAssessment16 elementsNo other package
HG001_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
HG001_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
HG001_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
HG001_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
Houston_1_PreSaved_DataMapObjAssessment16 elementsNo other package
Houston_1_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
Houston_1_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
Houston_1_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
Houston_1_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
Il1403_PreSaved_DataMapObjAssessment16 elementsNo other package
Il1403_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
Il1403_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
Il1403_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
Il1403_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
K_12_MG1655_PreSaved_DataMapObjAssessment16 elementsNo other package
K_12_MG1655_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
K_12_MG1655_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
K_12_MG1655_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
K_12_MG1655_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
LAL14_1_PreSaved_DataMapObjAssessment16 elementsNo other package
LAL14_1_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
LAL14_1_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
LAL14_1_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
LAL14_1_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
MG1363_PreSaved_DataMapObjAssessment16 elementsNo other package
MG1363_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
MG1363_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
MG1363_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
MG1363_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
MGAS5005_PreSaved_DataMapObjAssessment16 elements2 packages
MGAS5005_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
MGAS5005_PreSaved_ResultsObj_GeneMarkS2Assessment11 elements2 packages
MGAS5005_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
MGAS5005_PreSaved_ResultsObj_ProdigalAssessment11 elements2 packages
NCIB_3610_PreSaved_DataMapObjAssessment16 elementsNo other package
NCIB_3610_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
NCIB_3610_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
NCIB_3610_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
NCIB_3610_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
PAO1_PreSaved_DataMapObjAssessment16 elementsNo other package
PAO1_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
PAO1_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
PAO1_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
PAO1_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
SL1344_PreSaved_DataMapObjAssessment16 elementsNo other package
SL1344_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
SL1344_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
SL1344_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
SL1344_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
Strain10403S_PreSaved_DataMapObjAssessment16 elementsNo other package
Strain10403S_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
Strain10403S_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
Strain10403S_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
Strain10403S_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
Strain168_PreSaved_DataMapObjAssessment16 elementsNo other package
Strain168_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
Strain168_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
Strain168_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
Strain168_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package
TCH1516_PreSaved_DataMapObjAssessment16 elementsNo other package
TCH1516_PreSaved_ResultsObj_GenBankAssessment11 elementsNo other package
TCH1516_PreSaved_ResultsObj_GeneMarkS2Assessment11 elementsNo other package
TCH1516_PreSaved_ResultsObj_GlimmerAssessment11 elementsNo other package
TCH1516_PreSaved_ResultsObj_ProdigalAssessment11 elementsNo other package

All of AssessORFData's data objects

Topics

ExperimentData › OrganismData
ExperimentData › OrganismData › Bacillus_subtilis_Data
ExperimentData › OrganismData › Escherichia_coli_Data
ExperimentData › OrganismData › Pseudomonas_aeruginosa_Data
ExperimentData › OrganismData › Staphylococcus_aureus_Data
ExperimentData › SpecimenSource › Genome
ExperimentData › SpecimenSource › Proteome
ExperimentData › TechnologyData › SequencingData
Maintainer
Nicholas Cooley

Available on

CRANr2uBioconductorautoCRANCOPR

Suggested by (1)

AssessORF

People

Cite

Cite this package

Run in R for the authors' entry:

citation("AssessORFData")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btz714.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for AssessORFData version 1.30.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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