Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[pre-commit.ci] pre-commit autoupdate #49

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down Expand Up @@ -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"]
Expand All @@ -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]
Expand Down
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@

<!-- README.md is generated from README.Rmd. Please edit that file -->

# miplicorn <a href='https://bailey-lab.github.io/miplicorn/'><img src='man/figures/logo.png' align="right" height="139" /></a>
Expand All @@ -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)

<!-- badges: end -->

miplicorn establishes a unified analysis framework in R for molecular
Expand All @@ -27,7 +27,7 @@ You may install the package from

<div class=".pkgdown-release">

``` r
```r
# Install most recent released version
devtools::install_github("bailey-lab/[email protected]")
```
Expand All @@ -36,7 +36,7 @@ devtools::install_github("bailey-lab/[email protected]")

<div class=".pkgdown-devel">

``` r
```r
# Install development version
devtools::install_github("bailey-lab/miplicorn")
```
Expand All @@ -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")
Expand All @@ -74,7 +74,7 @@ plot_coverage(data, mutation_name)

<img src="man/figures/README-usage-1.png" width="100%" />

``` r
```r

prev <- mutation_prevalence(data, threshold = 5)
prev
Expand Down
45 changes: 45 additions & 0 deletions inst/WORDLIST
Original file line number Diff line number Diff line change
@@ -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
Loading