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  • Index fasta file generating fai file to use…

    femme rencontre sur belfort Index fasta file – generating fai file – to use with IGV or bedtools.

    samtools faidx reference.fasta

    http://genomeview.org/content/preparing-fasta-files

  • Convert all tabs to spaces and vice versa…

    Convert all tabs to spaces and vice versa.

    You can use the :retab command to convert all existing tabs to spaces. You can do both in one command:

    :set et|retab

    You can also convert spaces to tabs:

    :set noet|retab!

    http://vim.wikia.com/wiki/Super_retab

  • Vim plugin surround Normal mode ds delete a…

    Vim plugin surround

    Normal mode
    ———–
    ds – delete a surrounding
    cs – change a surrounding
    ys – add a surrounding
    yS – add a surrounding and place the surrounded text on a new line + indent it
    yss – add a surrounding to the whole line
    ySs – add a surrounding to the whole line, place it on a new line + indent it
    ySS – same as ySs

    Visual mode
    ———–
    s – in visual mode, add a surrounding
    S – in visual mode, add a surrounding but place text on new line + indent it

    http://www.catonmat.net/blog/vim-plugins-surround-vim/

  • http jeromyanglim blogspot ca 2010 05 abbreviations of…

    http://jeromyanglim.blogspot.ca/2010/05/abbreviations-of-r-commands-explained.html

    250+ R commands.
    Often times R users suffer from difficulties finding what commands are available for a specific process.
    This lists 250+ R commands in table.

  • Surround a VIM plugin that surrounds a word…

    Surround, a VIM plugin that surrounds a word or a line.

    http://www.catonmat.net/blog/vim-plugins-surround-vim/

  • Perl Getopt Long The module check wrong argument…

    Perl Getopt::Long.

    The module check wrong argument but does not check when no argument is provided.
    In order to check if there is no argument as well as wrong argument,
    check the argument also.

    GetOptions( 'test=s' => \$option_test )
    or exit(1);

defined($option_test)
    or die("Missing argument -t");

    http://www.perlmonks.org/?node_id=789974

  • Auto size of images in Beamer class \usepackage…

    Auto size of images in Beamer class.

    \usepackage{letltxmacro}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\makeatother
\AtBeginDocument{
  \LetLtxMacro\Oldincludegraphics\includegraphics
  \renewcommand{\includegraphics}[2][]{%
    \Oldincludegraphics[#1,width=\maxwidth]{#2}}
}

    http://tex.stackexchange.com/questions/67434/redefine-includegraphics-for-beamer#comment143600_67434

  • Beamer paper size is smaller than usual paper…

    Beamer paper size is smaller than usual paper size.
    The “paper size” of a beamer presentation is fixed to 128mm times 96mm.

    With this trick, the normal font can be shown nicely.
    But be cautious setting the image size with absolute value.
    or use

    \includegraphics[width=0.6\textwidth]{graphics.pdf}

    http://web.mit.edu/8.13/presentations/beameruserguide.pdf

    Citation

  • R color palettes # Basic grDevice rainbow topo…

    R color palettes

    1. Basic grDevice

    rainbow()
    topo.colors()
    terrain.colors()
    heat.colors()

    my.palette <- terrain.colors(100)
    1. RColoBrewer package
    display.brewer.all()

    my.palette <- brewer.pal(n, name) For example, my.palette <- brewer.pal(9, "Blues") However, the number of colors is limited up to 9, in most colors. Then use this. 

    more.color.palette <- colorRampPalette(brewer.pal(9,"Blues"))(100)

    http://stackoverflow.com/questions/3832850/color-schemes-in-r
    http://www.compbiome.com/2010/12/r-using-rcolorbrewer-to-colour-your.html

  • RColorBrewer palette names

    RColorBrewer palette names.