Including Bibliography in RMarkdown document with use of the knitcitations

If you want to include all references in the bibtex file, you can use, as mentioned by frankyan here

---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
nocite: '@*'
---

The @* is a wildcard for all references.

The pandoc documentation says:

If you want to include items in the bibliography without actually citing them in the body text, you can define a dummy nocite metadata field and put the citations there:

---
nocite: |
  @item1, @item2
...

@item3

In this example, the document will contain a citation for item3 only, but the bibliography will contain entries for item1, item2, and item3.

The entire chunk above (from --- to ...) can go anywhere in your code. @abichat prefers to put it after the YAML or in the Reference section.

Here is minimal working example:

paper.Rmd

---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
---

Application written in the R programming language [@RCoreTeam] using the Shiny framework [@Chang2015].

# REFERENCES

references.bib

@Misc{Chang2015,
  Title                    = {shiny: Web Application Framework for R. R package version 0.12.1},

  Author                   = {Chang, W. and Cheng, J. and Allaire, JJ. and Xie, Y. and McPherson, J. },
  Year                     = {2015},

  Type                     = {Computer Program},
  Url                      = {http://CRAN.R-project.org/package=shiny}
}


@Article{RCoreTeam,
  Title                    = {R: A Language and Environment for Statistical Computing},
  Author                   = {{R Core Team}},
  Year                     = {2015},

  Type                     = {Journal Article},
  Url                      = {http://www.R-project.org}
}

Console output

processing file: paper.Rmd
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS paper.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output paper.pdf --filter pandoc-citeproc --template "C:\Users\tdadaev\Documents\R\win-library\3.2\rmarkdown\rmd\latex\default.tex" --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in" --bibliography references.bib 
output file: paper.knit.md


Output created: paper.pdf

paper.pdf