Swarchal

import os

import czifile
import skimage.io
import numpy as np


def read_czi(fname):
    """shape: [1, 1, channel, z, x, y, 1]"""
    return fname, czifile.imread(fname)

Swarchal

import argparse
import sys
from random import choice
from string import ascii_letters
from time import sleep

charset = ascii_letters + '!@#$%^&*()[]<>./m::~`|\\"'


def scroll_text(text: str, delay: float = 0.01, n_chars: int = 5) -> None:

Swarchal

import pandas as pd
import numpy as np

def find_correlation(df, thresh=0.9):
    """
    Given a numeric pd.DataFrame, this will find highly correlated features,
    and return a list of features to remove

    params:
    - df : pd.DataFrame

Swarchal

import pandas as pd
import numpy as np

def find_correlation(data, threshold=0.9, remove_negative=False):
    """
    Given a numeric pd.DataFrame, this will find highly correlated features,
    and return a list of features to remove.
    Parameters
    -----------
    data : pandas DataFrame

Swarchal

import os
import tempfile
from collections import defaultdict
import string

import htsomeropy
import pandas as pd
from tqdm import tqdm

import cellprofiler_core.preferences as cpprefs

Swarchal

import os
from collections import namedtuple
from typing import NamedTuple, List
import pandas as pd

def parse_filepath(filepath: str) -> NamedTuple:
    """
    0|1|2|3|4|5|6|7|8|9|10|11|12|13|14|15|16|17|18|19|20
    T|0|0|0|1|F|0|0|6|L|0 |1 |A |0 |4 |Z |0 |1 |C |0 |2
    ------------------------------------------------------

Swarchal

library(ggplot2)
library(reshape2)

df_expression <- read.csv("expression.csv")
df_molten <- melt(df_expression)
ggplot(data = df_molten,
       aes(x = variable, y = MouseID, fill = value)) + 
    geom_raster() +
    xlab("Protein") + 
    scale_fill_distiller(palette = "RdYlBu", trans = "log10") +

Swarchal

class OnlineVariance:
    """Welfords online variance calculation"""

    def __init__(self, arr):
        self.arr = arr # np.array
        self.mean = arr
        self.count = 1
        self._M2 = 0

    def update(self, arr):

Swarchal

Swarchal

# install anaconda 5.10
! wget -c https://repo.continuum.io/archive/Anaconda3-5.1.0-Linux-x86_64.sh
! chmod +x Anaconda3-5.1.0-Linux-x86_64.sh
! bash ./Anaconda3-5.1.0-Linux-x86_64.sh -b -f -p /usr/local

import sys
sys.path.append('/usr/local/lib/python3.6/site-packages/')

# install conda dependencies
! conda install -y --prefix /usr/local pytorch==0.4.0 torchvision=0.1.8 -c pytorch