Keybase proof
I hereby claim:
- I am afrendeiro on github.
- I am afrendeiro (https://keybase.io/afrendeiro) on keybase.
- I have a public key ASCLj9Mi9QyGyaS_Ez-M1L2daTExlulKnwG2ltgD_v_mNwo
To claim this, I am signing this object:
#!/usr/bin/bash | |
# This script details an example of how to create an validate a PDF/A | |
# compatible PDF file for submission as a thesi at the Medical University | |
# of Vienna | |
# It assumes in the working directory there are ${PAPER}.initial.pdf files | |
# that will make up your cumulative thesis | |
# The first cause of failure for PDF/A compatibility is the PDFs from your |
#!/usr/bin/env python | |
""" | |
ChIP-seq pipeline | |
""" | |
from argparse import ArgumentParser | |
import os | |
import sys | |
import logging |
import numpy as np | |
import pandas as pd | |
import matplotlib.pyplot as plt | |
def gini(x): | |
# Mean absolute difference | |
mad = np.abs(np.subtract.outer(x, x)).mean() | |
# Relative mean absolute difference | |
rmad = mad / np.mean(x) |
#! /usr/bin/env python | |
""" | |
Convert 10X FASTQ files to single end BAM file with barcodes annotated as tags | |
""" | |
from argparse import ArgumentParser | |
from glob import glob |
I hereby claim:
To claim this, I am signing this object:
import scanpy.api as sc | |
import numpy as np | |
def add_tracker(field_name="tracker"): | |
from inspect import getcallargs | |
from functools import wraps | |
def tracker(f): | |
@wraps(f) | |
def wrapper(*args, **kwds): |
import pandas as pd | |
from sklearn.preprocessing import StandardScaler | |
# get list of genes of interest (e.g. from diff exp, or a known signature) | |
diff = pd.Index(['geneX', 'geneY']) | |
# X is our numeric matrix, shape (n_features, n_samples) | |
X = pd.DataFrame(index=['geneA', 'geneZ'], columns=['stimul_1', 'stimul_2'] + ['unstimul_1', 'unstimul_2']) | |
# Standardize and center |
>chr1 | |
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC | |
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC |
def plot_differential_enrichment( | |
enrichment_table, | |
enrichment_type, | |
data_type="ATAC-seq", | |
direction_dependent=True, | |
output_dir="results/differential_analysis_{data_type}/enrichments", | |
comp_variable="comparison_name", | |
output_prefix="differential_analysis", | |
rasterized=True, |
#!/usr/bin/env bash | |
# Dependencies: | |
# 1. inkscape | |
# 2. pdfunite | |
# 3. (optinal) minify (https://github.com/tdewolff/minify/tree/master/cmd/minify) | |
# `sudo apt install minify` | |
# Assumptions: | |
# 1. figures are made in SVG format |