soh-i

library(CytoML)
library(flowWorkspace)
library(ggcyto)

xmlfile <- 'gate.xml' # Gating-ML xml file generated by Cytobank
fcsFiles <- list.files(pattern='.fcs', path='./FCS/', full.names=TRUE)
gs <- cytobank2GatingSet(xmlfile, fcsFiles)
fs <- getData(gs, "P1") # FCS file object filtered by P1 gate (live cell)
P2 <- getGate(gs, "P2") # P2 gate object (EGFP gate)

soh-i

library(ggplot2)
library(RColorBrewer)

d <- read.csv('BC4-R1-1.fcs_spill_applied_AID_BC_Cell_P1.txt', sep='\t', header=T, skip=1)
names(d) <- c('Event', 'FSC', 'SCC', 'FITC')

myPalette <- colorRampPalette(rev(brewer.pal(11, "Spectral")), space="Lab")

g <- ggplot(d, aes(y=FSC, x=FITC)) +
    geom_hex(bins=128) +

soh-i

☕ Aichan ☕ >> python setup.py develop
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=--disable-lzma
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o

soh-i

#!/usr/bin/env perl

use strict;
use warnings;
use JSON;
use Data::Dumper;

my $file = shift or die('Input Data::Dumper output');

my $data = do $file;

soh-i

class BlastOut(object):
    def __init__(self, line):
        col = line.strip().split()
        self.col_string = line.strip()
        self.q = col[0]
        self.s = col[1]
        self.identity = float(col[2])
        self.alignment_len = int(col[3])
        self.mismatches = int(col[4])
        self.gap_open = int(col[5])

soh-i

pval.to.qual <- function(p) {
    return(-10*log10(p))
}

qual.to.pval <- function(q) {
    return(10^(-q/10))
}

LLR <- function(p, n, x) {

soh-i

// Soh Ishiguro

import ij.ImagePlus;
import ij.io.Opener;

public class Main {
    public static ImagePlus openImage(String filepath) {
        Opener op = new Opener();
        return op.openImage(filepath);
    }

soh-i

import random
import re

def generate_random_sequence(seq_length=20, n=10):
    """
    Random sequence generator.

    Args:
     seq_length: Int #sequence length
     n: Int #total number of sequences

soh-i

ls | grep filename_you_want_to_move  | xargs -J% cp -f % place_where_you_want

soh-i

import random
n_code = {0: "A", 1: "T", 2: "C", 3: "G"}
print "".join(map(lambda _: n_code[random.randint(0, 3)], range(0, 20)))