├── NAMESPACE ├── .gitignore ├── vignettes └── ZMakefile ├── DESCRIPTION └── README.md /NAMESPACE: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | vignettes/*html 2 | vignettes/*R 3 | vignettes/*_cache/ 4 | vignettes/*_files/ 5 | vignettes/Rplots.pdf 6 | -------------------------------------------------------------------------------- /vignettes/ZMakefile: -------------------------------------------------------------------------------- 1 | SOURCES = $(shell ls *Rmd) 2 | 3 | %.html: %.Rmd 4 | @echo "KNITR_CACHE=TRUE Sweave $<" 5 | @KNITR_CACHE=TRUE "$(R_HOME)"/bin/R --vanilla CMD Sweave $< 6 | 7 | %.R: %.Rmd 8 | @echo "KNITR_CACHE=FALSE Stangle $<" 9 | @KNITR_CACHE=FALSE && "$(R_HOME)"/bin/R --vanilla CMD Stangle $< 10 | 11 | all: $(SOURCES:.Rmd=.html) 12 | 13 | clean: 14 | rm -rf Rplots* *html *R *.md *_cache/ *_files/ figure/ 15 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: BiocIntro 2 | Type: Package 3 | Title: Training Material for Introductory R Courses 4 | Version: 0.0.8 5 | Authors@R: c( 6 | person("Martin", "Morgan", role=c("aut", "cre"), 7 | email="martin.morgan@roswellpark.org")) 8 | Description: Vignettes and resources to support introductory R 9 | training courses. 10 | Suggests: BiocStyle, knitr 11 | License: Artistic-2.0 12 | VignetteBuilder: knitr 13 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Introduction to _R_ and _Bioconductor_ 2 | 3 | [Bioconductor Course Material Archive][Bioc-archive] 4 | 5 | Recent courses: 6 | 7 | - [BiocAsia-2019][] - 1 1/2 hour introduction to Bioconductor for genomic analysis. 8 | - [CMCM-Nov-2019][] - 1 1/2 hour introduction to R and Bioconductor. 9 | - [UB-CDSE-Apr-2019][] - 2 hour tour of exploring large (cancer-related) data sets. 10 | - [NURDS-Apr-2019][] - 2 hour Developing robust and efficient code. 11 | - [BiocAsia-2018][] - 2 two-hour sessions on Annotation resources and package development. 12 | - [RPCI-Epigenome-Sept-2018][] - 1/2 day tour of _Bioconductor_ packages for epigenomics. 13 | - [Visby-2018][] - 4 presentations providing overviews of _Bioconductor_, core classes, annotation resources, and advanced aspects of classes and methods. 14 | - [OMRF-2017][] - 2 day introduction to _R_ and _Bioconductor_ 15 | - [UPSTAT-2017][] -- 1 two-hour session introducing _R_ and 16 | _Bioconductor_ through data exploration. 17 | - [CDSE-2017][] -- 1 three-hour session on high-throughput genomic analysis in 18 | _R_ and _Bioconductor_. 19 | - [Moffitt-2017][] -- 2 day introduction to _R_ and _Bioconductor_. 20 | - [RPCI-Jan-2017][] -- 5 one-hour sessions introduction _R_ to the 21 | Roswell Park community. 22 | - [Technion-2016][] -- 3 three-hour sessions introducing 23 | _Bioconductor_ (and _R_). 24 | 25 | [BiocAsia-2019]: https://github.com/Bioconductor/BiocIntro/blob/BiocAsia-2019/README.md 26 | [CMCM-Nov-2019]: https://github.com/Bioconductor/BiocIntro/blob/CMCM-2019/README.md 27 | [UB-CDSE-Apr-2019]: https://github.com/Bioconductor/BiocIntro/blob/UB-CDSE-Apr-2019/README.md 28 | [NURDS-Apr-2019]: https://github.com/Bioconductor/BiocIntro/blob/NURDS-Apr-2019/README.md 29 | [BiocAsia-2018]: https://github.com/Bioconductor/BiocIntro/blob/BiocAsia-2017/README.md 30 | [RPCI-Epigenome-Sept-2018]: https://github.com/Bioconductor/BiocIntro/blob/RPCI-Epigenome-Sept-2018/README.md 31 | [Visby-2018]: https://github.com/Bioconductor/BiocIntro/blob/visby-2018/README.md 32 | [OMRF-2017]: https://github.com/Bioconductor/BiocIntro/blob/OMRF-2017/README.md 33 | [UPSTAT-2017]: https://github.com/Bioconductor/BiocIntro/blob/UP-STAT-2017/vignettes/UPSTAT.Rmd 34 | [CDSE-2017]: https://github.com/Bioconductor/BiocIntro/blob/R-HTG-CDSE-Apr-2017/vignettes/R_HTS.Rmd 35 | [Moffitt-2017]: https://github.com/Bioconductor/BiocIntro/blob/Moffitt-2017/README.md 36 | [RPCI-Jan-2017]: https://github.com/Bioconductor/BiocIntro/blob/R-Intro-RPCI-Jan-2017/README.md 37 | [Technion-2016]: https://github.com/Bioconductor/BiocIntro/blob/Technion-2016/README.md 38 | [Bioc-archive]: https://bioconductor.org/help/course-materials 39 | --------------------------------------------------------------------------------