issue #13

mfansler · Sep 29, 2021 · 6492015 · 6492015
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^conda-recipe$
 ^\.github$
+^README\.Rmd$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,13 @@
 Package: txcutr
-Title: Transcriptome CutUTR
+Title: Transcriptome CUTteR
 Description: Various mRNA sequencing library preparation methods generate 
     sequencing reads from the transcript ends. Quantification of isoform usage 
     can be improved by using truncated versions of transcriptome annotations 
-    when assigning such reads to isoforms. This implements some convenience 
-    methods for readily generating such truncated annotations and their 
-    corresponding sequences.
+    when assigning such reads to isoforms. This package implements some 
+    convenience methods for readily generating such truncated annotations and 
+    their corresponding sequences.
 Version: 0.3.1
+Date: 2021-09-29
 Authors@R: 
     person(given = "Mervin",
            family = "Fansler",

diff --git a/README.Rmd b/README.Rmd
@@ -0,0 +1,130 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+    collapse = TRUE,
+    comment = "#>",
+    fig.path = "man/figures/README-",
+    out.width = "100%"
+)
+```
+
+# txcutr
+
+<!-- badges: start -->
+[![R build status](https://github.com/mfansler/txcutr/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/mfansler/txcutr/actions)
+[![Anaconda-Server Badge](https://anaconda.org/merv/r-txcutr/badges/installer/conda.svg)](https://conda.anaconda.org/merv)
+[![Anaconda-Server Badge](https://anaconda.org/merv/r-txcutr/badges/version.svg)](https://anaconda.org/merv/r-txcutr)
+<!-- badges: end -->
+
+## Overview
+
+Various mRNA sequencing library preparation methods generate sequencing reads 
+from the transcript ends. Quantification of isoform usage can be improved by 
+using truncated versions of transcriptome annotations when assigning such reads 
+to isoforms. The `txcutr` package implements some convenience methods for 
+readily generating such truncated annotations and their corresponding sequences.
+
+## Installation instructions
+
+**Interim Note:** This package is intended for release on Bioconductor, but is 
+currently only available through GitHub or Anaconda Cloud. 
+
+### Bioconductor
+Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `txcutr` using from [Bioconductor](http://bioconductor.org/) the following code:
+
+```{r 'install', eval = FALSE}
+if (!requireNamespace("BiocManager", quietly = TRUE)) {
+    install.packages("BiocManager")
+}
+
+## not currently available
+#BiocManager::install("txcutr")
+```
+
+And the development version from [GitHub](https://github.com/mfansler/txcutr) with:
+
+```{r 'install_dev', eval = FALSE}
+BiocManager::install("mfansler/txcutr")
+```
+
+### Conda/Mamba
+
+Users managing R environments with Conda/Mamba can install the package with:
+
+**Conda**
+```bash
+conda install -c conda-forge -c bioconda merv::r-txcutr
+```
+
+**Mamba**
+```bash
+mamba install -c conda-forge -c bioconda merv::r-txcutr
+```
+
+We strongly encourage users to create dedicated R environments. **Do not 
+install this in your *base* environment!**
+
+## Example
+
+A typical workflow for `txcutr` involves 
+
+ - loading an existing annotation as `TxDb` object
+ - truncating the annotation
+ - exporting the truncated annotation (GTF)
+ - exporting supporting files (FASTA, merge TSV)
+
+```{r eval=FALSE}
+library(rtracklayer)
+library(txcutr)
+library(BSgenome.Hsapiens.UCSC.hg38)
+
+## load human genome
+hg38 <- BSgenome.Hsapiens.UCSC.hg38
+
+## load human GENCODE annotation
+txdb <- makeTxDbFromGFF("gencode.v38.annotaton.gtf.gz", organism="Homo sapiens")
+
+## truncate to maximum of 500 nts
+txdb_w500 <- truncateTxome(txdb, maxTxLength=500)
+
+## export annotation
+exportGTF(txdb_w500, file="gencode.v38.txcutr_w500.gtf.gz")
+
+## export FASTA and merge-table
+exportFASTA(txdb_w500, genome=BSgenome.Hsapiens.UCSC.hg38, 
+            file="gencode.v38.txcutr_w500.fa.gz")
+exportMergeTable(txdb_w500, minDistance=200,
+                 file="gencode.v38.txcutr_w500.merge.tsv.gz")
+```
+
+## Citation
+
+Below is the citation output from using `citation('txcutr')` in R. Please
+run this yourself to check for any updates on how to cite __txcutr__.
+
+```{r 'citation', eval = requireNamespace('txcutr')}
+print(citation('txcutr'), bibtex = TRUE)
+```
+
+Please note that the `txcutr` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
+
+## Code of Conduct
+
+Please note that the `txcutr` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
+
+## Development tools
+
+* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
+* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
+* The [documentation website](http://mfansler.github.io/txcutr) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
+* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
+* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
+
+For more details, check the `dev` directory.
+
+This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
diff --git a/README.md b/README.md
@@ -0,0 +1,164 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# txcutr
+
+<!-- badges: start -->
+
+[![R build
+status](https://github.com/mfansler/txcutr/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/mfansler/txcutr/actions)
+[![Anaconda-Server
+Badge](https://anaconda.org/merv/r-txcutr/badges/installer/conda.svg)](https://conda.anaconda.org/merv)
+[![Anaconda-Server
+Badge](https://anaconda.org/merv/r-txcutr/badges/version.svg)](https://anaconda.org/merv/r-txcutr)
+<!-- badges: end -->
+
+## Overview
+
+Various mRNA sequencing library preparation methods generate sequencing
+reads from the transcript ends. Quantification of isoform usage can be
+improved by using truncated versions of transcriptome annotations when
+assigning such reads to isoforms. The `txcutr` package implements some
+convenience methods for readily generating such truncated annotations
+and their corresponding sequences.
+
+## Installation instructions
+
+**Interim Note:** This package is intended for release on Bioconductor,
+but is currently only available through GitHub or Anaconda Cloud.
+
+### Bioconductor
+
+Get the latest stable `R` release from
+[CRAN](http://cran.r-project.org/). Then install `txcutr` using from
+[Bioconductor](http://bioconductor.org/) the following code:
+
+``` r
+if (!requireNamespace("BiocManager", quietly = TRUE)) {
+    install.packages("BiocManager")
+}
+
+## not currently available
+#BiocManager::install("txcutr")
+```
+
+And the development version from
+[GitHub](https://github.com/mfansler/txcutr) with:
+
+``` r
+BiocManager::install("mfansler/txcutr")
+```
+
+### Conda/Mamba
+
+Users managing R environments with Conda/Mamba can install the package
+with:
+
+**Conda**
+
+``` bash
+conda install -c conda-forge -c bioconda merv::r-txcutr
+```
+
+**Mamba**
+
+``` bash
+mamba install -c conda-forge -c bioconda merv::r-txcutr
+```
+
+We strongly encourage users to create dedicated R environments. **Do not
+install this in your *base* environment!**
+
+## Example
+
+A typical workflow for `txcutr` involves
+
+-   loading an existing annotation as `TxDb` object
+-   truncating the annotation
+-   exporting the truncated annotation (GTF)
+-   exporting supporting files (FASTA, merge TSV)
+
+``` r
+library(rtracklayer)
+library(txcutr)
+library(BSgenome.Hsapiens.UCSC.hg38)
+
+## load human genome
+hg38 <- BSgenome.Hsapiens.UCSC.hg38
+
+## load human GENCODE annotation
+txdb <- makeTxDbFromGFF("gencode.v38.annotaton.gtf.gz", organism="Homo sapiens")
+
+## truncate to maximum of 500 nts
+txdb_w500 <- truncateTxome(txdb, maxTxLength=500)
+
+## export annotation
+exportGTF(txdb_w500, file="gencode.v38.txcutr_w500.gtf.gz")
+
+## export FASTA and merge-table
+exportFASTA(txdb_w500, genome=BSgenome.Hsapiens.UCSC.hg38, 
+            file="gencode.v38.txcutr_w500.fa.gz")
+exportMergeTable(txdb_w500, minDistance=200,
+                 file="gencode.v38.txcutr_w500.merge.tsv.gz")
+```
+
+## Citation
+
+Below is the citation output from using `citation('txcutr')` in R.
+Please run this yourself to check for any updates on how to cite
+**txcutr**.
+
+``` r
+print(citation('txcutr'), bibtex = TRUE)
+#> 
+#> To cite package 'txcutr' in publications use:
+#> 
+#>   Mervin Fansler (2021). txcutr: Transcriptome CUTteR. R package
+#>   version 0.3.1.
+#> 
+#> A BibTeX entry for LaTeX users is
+#> 
+#>   @Manual{,
+#>     title = {txcutr: Transcriptome CUTteR},
+#>     author = {Mervin Fansler},
+#>     year = {2021},
+#>     note = {R package version 0.3.1},
+#>   }
+```
+
+Please note that the `txcutr` was only made possible thanks to many
+other R and bioinformatics software authors, which are cited either in
+the vignettes and/or the paper(s) describing this package.
+
+## Code of Conduct
+
+Please note that the `txcutr` project is released with a [Contributor
+Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By
+contributing to this project, you agree to abide by its terms.
+
+## Development tools
+
+-   Continuous code testing is possible thanks to [GitHub
+    actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
+    through *[usethis](https://CRAN.R-project.org/package=usethis)*,
+    *[remotes](https://CRAN.R-project.org/package=remotes)*, and
+    *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)*
+    customized to use [Bioconductor’s docker
+    containers](https://www.bioconductor.org/help/docker/) and
+    *[BiocCheck](https://bioconductor.org/packages/3.13/BiocCheck)*.
+-   Code coverage assessment is possible thanks to
+    [codecov](https://codecov.io/gh) and
+    *[covr](https://CRAN.R-project.org/package=covr)*.
+-   The [documentation website](http://mfansler.github.io/txcutr) is
+    automatically updated thanks to
+    *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
+-   The code is styled automatically thanks to
+    *[styler](https://CRAN.R-project.org/package=styler)*.
+-   The documentation is formatted thanks to
+    *[devtools](https://CRAN.R-project.org/package=devtools)* and
+    *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
+
+For more details, check the `dev` directory.
+
+This package was developed using
+*[biocthis](https://bioconductor.org/packages/3.13/biocthis)*.