- 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.
View 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 |
View 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) |
View nih_grant_link_eracommons.md
View 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 |
View 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()] |
View 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 |
View seaborn_clustermap_with_effortless_colorbars_decorator.ipynb
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View 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]) |
View 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 |
View 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 |
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