a new beginning

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^README\.Rmd$
+^LICENSE\.md$

.github/.gitignore

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+*.html

.github/workflows/R-CMD-check.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          #- {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          #- {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: bcbioR
+Type: Package
+Title: Templates and functions to guide downstream analysis and data interpretation
+Version: 0.1.0
+Authors@R: person("Pantano", "Lorena", , "[email protected]",
+            role = c("aut", "cre"))
+Description: Collaborative code repository from the Harvard Chan Bioinformatics Core.
+License: MIT + file LICENSE
+LazyData: true
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2024 Blue Collar Bioinformatics
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: bcbioR authors

LICENSE.md

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+# MIT License
+
+Copyright (c) 2024 bcbioR authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/hello.R

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+# Hello, world!
+#
+# This is an example function named 'hello' 
+# which prints 'Hello, world!'.
+#
+# You can learn more about package authoring with RStudio at:
+#
+#   http://r-pkgs.had.co.nz/
+#
+# Some useful keyboard shortcuts for package authoring:
+#
+#   Install Package:           'Cmd + Shift + B'
+#   Check Package:             'Cmd + Shift + E'
+#   Test Package:              'Cmd + Shift + T'
+
+hello <- function() {
+  print("Hello, world!")
+}

README.Rmd

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+---
+output: github_document
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# bcbioR
+
+<!-- badges: start -->
+  [![R-CMD-check](https://github.com/bcbio/bcbioR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcbio/bcbioR/actions/workflows/R-CMD-check.yaml)
+  <!-- badges: end -->
+
+The goal of bcbioR is to ...
+
+## Installation
+
+You can install the development version of bcbioR from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("bcbio/bcbioR")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+library(bcbioR)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
+
+```{r cars}
+summary(cars)
+```
+
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this.
+
+You can also embed plots, for example:
+
+```{r pressure, echo = FALSE}
+plot(pressure)
+```
+
+In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

README.md

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+
+# bcbioR
+
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/bcbio/bcbioR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcbio/bcbioR/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+The goal of bcbioR is to …
+
+## Installation
+
+You can install the development version of bcbioR from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("bcbio/bcbioR")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(bcbioR)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`?
+You can include R chunks like so:
+
+``` r
+summary(cars)
+#>      speed           dist       
+#>  Min.   : 4.0   Min.   :  2.00  
+#>  1st Qu.:12.0   1st Qu.: 26.00  
+#>  Median :15.0   Median : 36.00  
+#>  Mean   :15.4   Mean   : 42.98  
+#>  3rd Qu.:19.0   3rd Qu.: 56.00  
+#>  Max.   :25.0   Max.   :120.00
+```
+
+You’ll still need to render `README.Rmd` regularly, to keep `README.md`
+up-to-date. `devtools::build_readme()` is handy for this.
+
+You can also embed plots, for example:
+
+<img src="man/figures/README-pressure-1.png" width="100%" />
+
+In that case, don’t forget to commit and push the resulting figure
+files, so they display on GitHub and CRAN.

inst/rmarkdown/templates/rnaseq_qc/skeleton/params_de.R

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+# info params
+project = "name_hbcXXXXX"
+PI = 'person name'
+experiment = 'short description'
+aim = 'short description'
+analyst = 'person in the core'
+
+# project params
+root = "../"
+date = "YYYYMMDD"
+column = "treatment"
+subset_column = 'cell'
+metadata_fn = "../meta/samplesheet.csv"
+counts_fn = '../data/tximport-counts.csv'
+basedir <- 'reports'