André F. Rendeiro afrendeiro

## seaborn_clustermap_with_effortless_colorbars_decorator.ipynb

      
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                afrendeiro
                / seaborn_clustermap_with_effortless_colorbars_decorator.ipynb
            
            
              Last active May 14, 2020
            
              
                Seaborn clustermap with effortless row and column colorbars
              
          
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## easier_pandas_multiindex_getitem.py
import pandas as pd
import seaborn as sns


class Loc:
    def __init__(self, pandas_obj):
        self._obj = pandas_obj
    def __getitem__(self, x):
        return pd.Index(self._obj.index.to_frame().loc[x])

## guides_to_ref.py
#!/usr/bin/env python

"""
This script generates a transcriptome reference with additional
scaffolds/chromosomes for CRISPR gRNA constructs.
"""

import sys
import os
from argparse import ArgumentParser

## create_reference_genome_mixtures.py
#!/usr/bin/env python


"""
This script creates reference genomes with mixtures of organisms/assemblies.
"""

import sys
import os
import argparse

## make_validate_pdfa_muw.sh
#!/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

## chipseq_pipeline.py
#!/usr/bin/env python

"""
ChIP-seq pipeline
"""

from argparse import ArgumentParser
import os
import sys
import logging

## distributions_gini_lorenz_curves.py
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)

## 10Xfastq_to_bam.py
#! /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

## keybase.md

      
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                afrendeiro
                / keybase.md
            
            
              Created Mar 12, 2019
            
              
                keybase confirmation
              
          
      View keybase.md
  
      
    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:

  
## add_tracking_to_scanpy.py
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
	import seaborn as sns


	class Loc:
	def __init__(self, pandas_obj):
	self._obj = pandas_obj
	def __getitem__(self, x):
	return pd.Index(self._obj.index.to_frame().loc[x])
	#!/usr/bin/env python

	"""
	This script generates a transcriptome reference with additional
	scaffolds/chromosomes for CRISPR gRNA constructs.
	"""

	import sys
	import os
	from argparse import ArgumentParser
	#!/usr/bin/env python


	"""
	This script creates reference genomes with mixtures of organisms/assemblies.
	"""

	import sys
	import os
	import argparse
	#!/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
	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):