diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 892bd6c..6eb2dd3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
repos:
# R specific hooks
- repo: https://github.com/lorenzwalthert/precommit
- rev: v0.3.2
+ rev: v0.4.3.9001
hooks:
- id: style-files
args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -55,7 +55,7 @@ repos:
# Check large files, add newline to end of file, and trim trailing whitespace
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.3.0
+ rev: v5.0.0
hooks:
- id: check-added-large-files
args: ["--maxkb=200"]
@@ -66,7 +66,7 @@ repos:
# Style markdown and yaml
- repo: https://github.com/pre-commit/mirrors-prettier
- rev: v2.7.1
+ rev: v4.0.0-alpha.8
hooks:
- id: prettier
types_or: [yaml, markdown]
diff --git a/README.md b/README.md
index ccc750d..9cbac94 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,3 @@
-
# miplicorn
@@ -12,6 +11,7 @@ coverage](https://codecov.io/gh/bailey-lab/miplicorn/branch/main/graph/badge.svg
experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![License:
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
miplicorn establishes a unified analysis framework in R for molecular
@@ -27,7 +27,7 @@ You may install the package from
-``` r
+```r
# Install most recent released version
devtools::install_github("bailey-lab/miplicorn@v0.2.1")
```
@@ -36,7 +36,7 @@ devtools::install_github("bailey-lab/miplicorn@v0.2.1")
-``` r
+```r
# Install development version
devtools::install_github("bailey-lab/miplicorn")
```
@@ -48,7 +48,7 @@ devtools::install_github("bailey-lab/miplicorn")
See `vignette("miplicorn")` for a more extensive introduction and a
demonstration of several features of the package.
-``` r
+```r
library(miplicorn)
ref_file <- miplicorn_example("reference_AA_table.csv")
@@ -74,7 +74,7 @@ plot_coverage(data, mutation_name)
-``` r
+```r
prev <- mutation_prevalence(data, threshold = 5)
prev
diff --git a/inst/WORDLIST b/inst/WORDLIST
index 457b5c0..73a5efc 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,42 +1,87 @@
Amplicon
amplicon
+Aris
+arispas
+bootswatch
+bslib
+cgi
CMD
Codecov
+codecov
colour
coloured
colours
+config
+covr
dbplyr
+desc
dplyr
dtplyr
+env
erroring
eval
extdata
falciparum
+faq
filepath
+Fira
+gff
ggplot
+gh
Github
+github
+haplotyping
+href
+http
+https
+io
+JamesIves
karyoplot
karyoploteR
+Lato
Lifecycle
+macOS
magrittr
+MERCHANTABILITY
Metaprogramming
MIP
miplicorn
MIPTools
MIPtools
+monospace
NaN
+nav
+navbar
+ncbi
+nih
+nlm
+NONINFRINGEMENT
+oldrel
ORCID
+os
+pandoc
+Paschalidis
pkgdown
PlasmoDB
Plasmodium
pts
+px
+rcmdcheck
README
rect
+Reprex
rlang
+Rscript
+rspm
signalling
+sublicense
+tbl
tibble
TSV
tunnelled
tunnelling
+ubuntu
UMI
umi
+www
+wwwtax