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Saket Choudhary saketkc

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@brantfaircloth
brantfaircloth / get_protein.py
Created Apr 3, 2011
Get protein sequences from Genbank given a genomic accession number and a gene name
View get_protein.py
import sys
import time
from Bio import Entrez
Entrez.email = "your.email@domain.tld"
if not Entrez.email:
print "you must add your email address"
sys.exit(2)
# create an empty list we will fill with the gene names
@saketkc
saketkc / TEST.rb
Created Jul 14, 2011
CodeChef(SPOJ) Problem1 Ruby Solution
View TEST.rb
a=[]
while STDIN.readline.chomp!="42"
a.push($_)
end
a.each { |s| puts s }
@brentp
brentp / one-channel-agilent.R
Created Aug 17, 2011
use limma to normalize 1-channel agilent data and write out differentially expressed genes.
View one-channel-agilent.R
library(limma)
GROUP="62976"
# targets.txt has columns of "FileName" and "Condition" e.g.
"""
FileName Condition
data/scrubbed/LT001098RU_COPD.45015.txt COPD
data/scrubbed/LT001600RL_ILD.45015.txt ILD
data/scrubbed/LT003990RU_CTRL.45015.txt CTRL
data/scrubbed/LT004173LL_ILD.45015.txt ILD
View tmux-cheatsheet.markdown

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname
@willurd
willurd / web-servers.md
Last active Jan 19, 2022
Big list of http static server one-liners
View web-servers.md

Each of these commands will run an ad hoc http static server in your current (or specified) directory, available at http://localhost:8000. Use this power wisely.

Discussion on reddit.

Python 2.x

$ python -m SimpleHTTPServer 8000
View kernel_kmeans.py
"""Kernel K-means"""
# Author: Mathieu Blondel <mathieu@mblondel.org>
# License: BSD 3 clause
import numpy as np
from sklearn.base import BaseEstimator, ClusterMixin
from sklearn.metrics.pairwise import pairwise_kernels
from sklearn.utils import check_random_state
@gizmaa
gizmaa / Plot_Examples.md
Last active Jan 22, 2022
Various Julia plotting examples using PyPlot
@fperez
fperez / ProgrammaticNotebook.ipynb
Last active Dec 9, 2021
Creating an IPython Notebook programatically
View ProgrammaticNotebook.ipynb
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View goto_powered.py
# Inspired by the following sentence that I ran across this morning:
#
# "f_lineno is the current line number of the frame - writing to
# this from within a trace function jumps to the given line
# (only for the bottom-most frame). A debugger can implement a
# Jump command (aka Set Next Statement) by writing to f_lineno."
#
# https://docs.python.org/2/reference/datamodel.html
#
# There is an older implementation of a similar idea:
@dgrtwo
dgrtwo / mnist_pairs.R
Created May 31, 2017
Comparing pairs of MNIST digits based on one pixel
View mnist_pairs.R
library(tidyverse)
# Data is downloaded from here:
# https://www.kaggle.com/c/digit-recognizer
kaggle_data <- read_csv("~/Downloads/train.csv")
pixels_gathered <- kaggle_data %>%
mutate(instance = row_number()) %>%
gather(pixel, value, -label, -instance) %>%
extract(pixel, "pixel", "(\\d+)", convert = TRUE)