maftools
Bioc currentSummarize, Analyze and Visualize MAF Files
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
159 78 exported
Complexity
9 avg / 46 max
Call network
159 nodes / 151 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
22,021
Files
240
Compiled share
3.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
78
Internal functions
67
Recent export changes
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
6%
Unsafe pattern score
11
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3
System requirements
2 externalGNU make, curl
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2017-03-13
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
23
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 85
- Examples that run
- 87%55 run in a plain check · 8 never run
- Exported functions with examples
- 75%
- Documented parameters
- 100%
- Return-value docs
- 81%
- Help pages citing references
- 24%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/poisonalien/maftools on 2026-10-11.
The R CMD check workflow runs on Linux
The repository owner accepts GitHub Sponsors
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| BP_SMGs | – | – | – |
| LAML_CBS_segments | – | – | – |
| LAML_sig_genes | data.frame | 18,253 × 19 | No other package |
| SBS_signatures | list | 2 elements | No other package |
| SBS_v34_signatures | list | 2 elements | No other package |
| TCGA.AB.3009.hg19.seg | data.frame | 818 × 6 | No other package |
| all_lesions.conf_99 | data.frame | 32 × 201 | No other package |
| amp_genes.conf_99 | data.frame | 39 × 6 | No other package |
| cancerhotspots_v2_GRCh37 | data.frame | 3,180 × 8 | No other package |
| cancerhotspots_v2_GRCh38 | data.frame | 3,180 × 8 | No other package |
| cancerhotspots_v2_hg19 | data.frame | 3,180 × 8 | No other package |
| cancerhotspots_v2_hg38 | data.frame | 3,180 × 8 | No other package |
| categories | data.frame | 20,075 × 4 | No other package |
| del_genes.conf_99 | data.frame | 1,004 × 14 | No other package |
| drugs | – | – | – |
| ensGenes | data.frame | 57,773 × 3 | No other package |
| hg19_cytobands | data.frame | 861 × 5 | No other package |
| hg19_smash_snps | – | – | – |
| hg38_cytobands | – | – | – |
| hg38_smash_snps | – | – | – |
| hugo_to_mutSigSymbol | data.frame | 1,300 × 2 | No other package |
| legacy_signatures | list | 2 elements | No other package |
| oncogenic_sig_patwhays | data.frame | 335 × 3 | No other package |
| pancan | data.frame | 260 × 2 | No other package |
| prot_len | data.frame | 18,251 × 4 | No other package |
| protein_domains | data.table | 92,849 × 12 | No other package |
| simple_somatic_mutation.open.ESCA-CN.sample | data.frame | 499 × 42 | No other package |
| tcga_cohort | – | – | – |
| tcga_laml_annot | data.frame | 200 × 4 | No other package |
| variants | data.frame | 10 × 6 | No other package |
| variants.hg19_multianno | data.frame | 10 × 11 | No other package |
Topics
Depended on by (13)
Show all 18 packagesHide all 18 packages
Bioconductor (8)
CRAN (5)
Suggested by (5)
People
- Anand Mayakonda author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("maftools")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/gr.239244.118.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.