André F. Rendeiro afrendeiro

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

"""
Upload images inside zip files to box.com.
"""

import sys, time, webbrowser, json, zipfile, tempfile, urllib3
from argparse import ArgumentParser
from pathlib import Path
from typing import Dict, List, Generator

## dog_ex.py
from skimage import data, feature, color, filters, img_as_float
from matplotlib import pyplot as plt


original_image = img_as_float(data.chelsea())
img = color.rgb2gray(original_image)

k = 1.6

plt.subplot(2,3,1)

## nih_grant_link_eracommons.md

      
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                afrendeiro
                / nih_grant_link_eracommons.md
            
            
              Last active Dec 28, 2020
            
              
                Linking NIH grant number to publications in NCBI/eRA Commons
              
          
      View nih_grant_link_eracommons.md
  
      
An important first step is to link the era commons and the NCBI accounts. Check if linked here: https://www.ncbi.nlm.nih.gov/account/settings/ and link accounts here: https://www.ncbi.nlm.nih.gov/account/settings/linked-accounts/.
One that is done, go to your bibliography page of NCBI (https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/).
In there should be your publications, if not, search and add it manually with "Add citations".
For each citation there is a panel on the right that has the grant awards mentioned in the work or a "Add Award" button to add manually.


## series_matrix2csv.py
#!/usr/bin/env python

"""
Get a GEO series matrix file describing an experiment and
parse it into project level and sample level data.
"""

import os
from typing import Tuple, Union
import tempfile

## get_gene_set_libraries.py
from pathlib import Path

import parmap
import requests


def update(gsll):
    return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()]

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

"""
Max-reduce and stitch microscopy images into one stitched one.

Requirements:
`pip install numpy matplotlib tifffile`
"""

from pathlib import Path

## 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
              
          
      View seaborn_clustermap_with_effortless_colorbars_decorator.ipynb
  
    
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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
	#!/usr/bin/env python

	"""
	Upload images inside zip files to box.com.
	"""

	import sys, time, webbrowser, json, zipfile, tempfile, urllib3
	from argparse import ArgumentParser
	from pathlib import Path
	from typing import Dict, List, Generator
	from skimage import data, feature, color, filters, img_as_float
	from matplotlib import pyplot as plt


	original_image = img_as_float(data.chelsea())
	img = color.rgb2gray(original_image)

	k = 1.6

	plt.subplot(2,3,1)
	#!/usr/bin/env python

	"""
	Get a GEO series matrix file describing an experiment and
	parse it into project level and sample level data.
	"""

	import os
	from typing import Tuple, Union
	import tempfile
	from pathlib import Path

	import parmap
	import requests


	def update(gsll):
	return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()]
	#!/usr/bin/env python

	"""
	Max-reduce and stitch microscopy images into one stitched one.

	Requirements:
	`pip install numpy matplotlib tifffile`
	"""

	from pathlib import Path
	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