documentclass[12, twoside]{report}
usepackage{textcomp}
usepackage{graphicx}
usepackage[a4paper,margin=1in]{geometry}
begin{document}
graphicspath{{./Figures/}}

begin{figure}[htbp]
includegraphics[width=textwidth]{Figure1.pdf}
caption[short]{textbf{Cancer incidences of different age groups in Canada for 2010.} For both men and women, the five cancer types with the highest incidence rates of new primary cancer were plotted. This figure shows that incidence rates increase with age, indicating that cancer requires decades to progress in adults. textit{Data: CANSIM table 103-0550, Statistics Canada. Accessed: April 4th, 2015}}
end{figure}

clearpage
begin{figure}[htbp]
includegraphics[width=textwidth]{Figure2.png}
caption{textbf{Canadian women breast cancer estimates.} It is expected that approximately 1/9 women will be diagnosed with breast cancer during her lifetime, and 1/30 will die from it. textit{Source: Canadian Cancer Society's 2009 estimates.}}
end{figure}

clearpage
begin{figure}[htbp]
includegraphics[width=textwidth]{Figure3.pdf}
caption{textbf{Log-log plots of cancer mortality rates in Canada for 2010.} This figures shows that cancer overall requires at least six steps for both men and women (A,B). Additionally, the mathematical modelling of the influence and fluctuating estrogen levels on breast cancer is consistent with the epidemiological data (C). Colon cancer in women is used as control because it is hormonally independent (D). textit{Data: CANSIM tables 051-0522 and 102-0522, Statistics Canada. Accessed: April 4th, 2015}}
end{figure}

clearpage
begin{figure}[htbp]
includegraphics[width=textwidth]{Ur.pdf}
caption[short]{textbf{Ziggurat of Ur.} This Ziggurat was built during the 21st century BC by the neo-Sumerians in the city (now ruins) of Ur, Irak in honor of their moon God, Nanna (A). It originally
had three main levels, but only two now remain (B). Several restoration efforts have been carried out. The sketch was drawn by British archaeologist Sir Leonard Woolley who excavated Ur in the 1920s. Interestingly, he proposed that Ur was Ur of Chaldees, the birthplace of the biblical patriarch Abraham (Genesis 11:31). While hoping to uncover Abraham's home, Woolley famously found the Ur's royal cemetery that included ~2000 burials. textit{Source: http://oracc.museum.upenn.edu/amgg/listofdeities/nannasuen/, http://www.penn.museum/press-releases/650-iraqs-ancient-past-press-release.html, Bible. Accessed: May 11th, 2015}}
end{figure}

clearpage
begin{figure}[htbp]
includegraphics[width=textwidth]{boxplots.pdf}
caption[short]{textbf{Identification of Arm-level and Focal Events of Claudin-low tumors in METABRIC}}
end{figure}


begin{figure}[htbp]
includegraphics[width=textwidth]{rawCopy.jpg}
caption[short]{textbf{Raw copy number of claudin-low tumors}}
end{figure}

end{document}

documentclass{article}
usepackage{tikz,subcaption}
usetikzlibrary{positioning}

begin{document}
% Vertical flip
begin{figure}
   begin{subfigure}[b]{.5textwidth}
     begin{tikzpicture}
         node[scale=0.4] (a)
         { scalebox{1}[1]{includegraphics[scale=1]{example-image-a}} };
     end{tikzpicture}
     caption{}
   end{subfigure}
   begin{subfigure}[b]{.5textwidth}
     begin{tikzpicture}
         node[scale=0.4] (a)
         { scalebox{1}[-1]{includegraphics[scale=1]{example-image-a}} };
      end{tikzpicture}
      caption{}
   end{subfigure}
caption{Vertical flip of .jpg or .pdf files}
end{figure}
% Horizontal flip
begin{figure}
   begin{subfigure}[b]{.5textwidth}
      begin{tikzpicture}
          node[scale=0.4] (a)
          { scalebox{1}[1]{includegraphics[scale=1]{example-image-b}} };
      end{tikzpicture}
      caption{}
    end{subfigure}
    begin{subfigure}[b]{.5textwidth}
      begin{tikzpicture}
         node[scale=0.4] (a)
         { scalebox{-1}[1]{includegraphics[scale=1]{example-image-b}} };
      end{tikzpicture}
    caption{}
  end{subfigure}
caption{Horizontal flip of .jpg or .pdf files}
end{figure}
end{document}

According to the EXIF data, this image is rotated.
Would you like GIMP to rotate it into the standard orientation?