Puriney

Minimal R shiny app demonstrating:

1. how to upload a CSV file into an R/shiny app
2. how to automatically populate list selectors based on column headers
3. how to use optional list selectors
4. how to populate a list selector with column names of numerical columns only
5. how to use an action button to trigger an event when you're ready to do so

---

Puriney

install open-babel

brew install open-babel

locate OPEN_BABEL_INCDIR and OPEN_BABEL_LIBDIR

OPEN_BABEL_INCDIR is /usr/local/Cellar/open-babel/2.3.2/lib/openbabel/2.3.2, where files like alias.h, descriptor.h, pointgroup.h, atom.h etc.

OPEN_BABEL_LIBDIR is /usr/local/Cellar/open-babel/2.3.2/lib/openbabel/2.3.2, where files like APIInterface.so, fastsearchformat.so, outformat.so, CSRformat.so, etc.

Puriney

" don't bother with vi compatibility
set nocompatible
" Color Scheme
" enable syntax highlighting
syntax enable
set background=dark
" configure Vundle
filetype on " without this vim emits a zero exit status, later, because of :ft off
filetype off
set rtp+=~/.vim/bundle/vundle/

Puriney

library(GenomicRanges)

sampleChr <- paste0("Chr", 1:3)
sampleStarts <- sample(1:100, size = 3, replace = F)
sampleEnds <- sampleStarts + 10 
sampleStrand <- sample(c("+", "-"), size = 3, replace = T)

sampleValue <- rnorm(3)
sampleGR1 <- GRanges(seqnames = Rle(sampleChr), ranges = IRanges(sampleStarts, sampleEnds), strand = Rle(sampleStrand), value = sampleValue)
sampleGR2 <- GRanges(seqnames = Rle(sampleChr), ranges = IRanges(sampleStarts + 10 , sampleEnds + 100), strand = Rle(sampleStrand), value = sampleValue)

Puriney

# Pretty git log
# https://github.com/tiimgreen/github-cheat-sheet/blob/master/README.zh-cn.md#%E6%9B%B4%E7%9B%B4%E8%A7%82%E7%9A%84git-log
# echo $0 >> ~/.bash_profile
alias gitlog="git log --all --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit --date=relative"

Puriney

%!TEX TS-program = xelatex
\documentclass[12pt]{scrartcl}  

% The declaration of the document class:

% The second line here, i.e.
% \documentclass[12pt]{scrartcl} 
% is a standard LaTeX document class declaration: 
% we say what kind of document we are making in curly brackets, 
% and specify any options in square brackets.

Puriney

<div class="panel-group" id="accordion">
  <div class="panel panel-default">
    <div class="panel-heading">
      <h4 class="panel-title">
        <a class="accordion-toggle" data-toggle="collapse" data-parent="#accordion" href="#collapseOne">
          Accordian1
        </a>
      </h4>
    </div>
    <div id="collapseOne" class="panel-collapse collapse in">

Puriney

## Demo for HMM
## Reproduce "What is HMM", Sean R Eddy, Nature Biotechnology 2004

S <- c(0,1,rep(0,3))
E <- c(0, 0.9, 0.1, 0, 0)
SS5 <- c(rep(0,3), 1, 0)
I <- c(rep(0,3), 0.9, 0.1)
N <- c(rep(0,4), 1)
myTransMtx <- rbind(S,E, SS5, I, N)
colnames(myTransMtx) <- rownames(myTransMtx)

Puriney

library(ShortRead)

# Root of .bam filename
sname <- "HG00100.unmapped.ILLUMINA.bwa.GBR.low_coverage.20130415"

# Construct path to file
fname <- file.path("alignments",paste(sname,".bam",sep=""))

# Read alignments
bm <- readGappedAlignments(fname)

Puriney

#!/usr/bin/perl -w 
use strict;

# Notice: 
# BED annotation should be sorted by the GeneID or GeneName ahead
# otherwise duplication in output 
my $inBed = shift || die $!;
my $outUnion = shift || die $!;

open OUT, "> $outUnion";