Sergey Venev sergpolly
sergpolly
/ snip_helpers.py
Created
February 14, 2024 14:50
helper functions for snipping module in cooltools
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| def triu(arr, value=np.nan, k=0, copy=False): | |
| """ | |
| Upper triangle of an array. | |
| Modifies input array, such that its elements below the k-th diagonal | |
| are filled with value (returns modified copy, when requested instead). | |
| Assumes that the input array is 2D. | |
| Parameters | |
| ---------- |
sergpolly
/ oe_matrix_fetcher_inherit.ipynb
Last active
February 1, 2024 20:23
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sergpolly
/ oe_matrix_fetcher.ipynb
Created
January 31, 2024 21:34
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| import pandas as pd | |
| import numpy as np | |
| from itertools import combinations | |
| from functools import partial | |
| from scipy.linalg import toeplitz | |
| import pandas as pd | |
| from cooltools.lib.checks import ( | |
| is_compatible_viewframe, | |
| is_valid_expected, | |
| is_cooler_balanced, |
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| f = clr.open('r') | |
| reader = cooler.core._rangequery.CSRReader(f['pixels'], f['indexes/bin1_offset'][:]) | |
| sel = cooler.core._rangequery.DirectRangeQuery2D(reader, "count", bbox=[0,1000,0,1000], chunksize=1_000_000) | |
| sel_low = cooler.core._rangequery.FillLowerRangeQuery2D(reader, "count", bbox=[0,1000,0,1000], chunksize=1_000_000) | |
| cooler.core._rangequery.FillLowerRangeQuery2D | |
| plt.imshow(np.log(sel_low.to_array())) | |
| sel.tasks | |
| for g in sel: | |
| print(g) |
sergpolly
/ dots-dump-scores.ipynb
Created
February 3, 2023 22:39
dotfinder based notebook that ends with an iterator of scored pixels
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sergpolly
/ JointEigendecomposition.ipynb
Created
March 11, 2021 18:50
attempt at join eigendecomposition on 2 samples
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sergpolly
/ expected_schema_region_table.ipynb
Created
March 1, 2021 22:09
trying schemas for expected and sanitized reading (region_table guaranteed)
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sergpolly
/ try_intpolated_expected.ipynb
Created
February 17, 2021 16:42
checking out Max's logbin_expected PR - mostly about the dense mat_expected editing
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