GPN-MSA
Collection
https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1
•
9 items
•
Updated
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1
Datasets:
chrom
large_stringlengths 1
2
| pos
int64 14.9k
249M
| ref
large_stringlengths 1
1
| alt
large_stringlengths 1
1
| label
bool 2
classes | GPN-MSA
float32 -13.38
12.6
| CADD
float64 -8.77
4.33
| phyloP-100v
float64 -10
20
⌀ | phyloP-241m
float64 -8.9
20
⌀ | phastCons-100v
float64 -1
-0
⌀ | ESM-1b
float64 -19.5
12
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|
1 | 69,511 | A | G | false | 1.493164 | -0.112916 | 0.684 | -3.29 | -0 | null |
1 | 953,279 | T | C | false | 2.578125 | -0.266107 | -0.037 | -1.27 | -0.009 | -2.88 |
1 | 973,858 | G | C | false | 1.5625 | -0.787153 | 0.431 | -0.835 | -0 | -2.538 |
1 | 973,929 | T | C | false | -1.328125 | -0.818047 | -0.076 | 0.539 | -0.001 | -3.377 |
1 | 976,215 | A | G | false | -2.527344 | -1.476529 | -0.054 | 0.421 | -0 | -5.335 |
1 | 978,953 | C | G | false | 1.72168 | 0.096301 | 0.22 | 0.223 | -0 | -3.781 |
1 | 999,842 | C | A | false | -1.387695 | -0.472275 | 0.582 | 1.508 | -0 | null |
1 | 1,014,228 | G | A | false | -2.003906 | -0.027262 | 0.396 | 0.787 | -0 | -4.136 |
1 | 1,072,052 | G | A | false | -0.551758 | 0.862209 | 1.398 | 4.07 | -0 | -5.237 |
1 | 1,179,288 | G | A | false | 0.321289 | -0.167083 | 0.447 | -0.13 | -0 | -3.748 |
1 | 1,180,851 | T | C | false | 1.851563 | -0.21429 | -0.026 | -1.845 | -0 | -2.236 |
1 | 1,197,558 | G | A | false | -2.478516 | -1.409054 | -1.648 | -0.167 | -0.014 | -7.455 |
1 | 1,211,863 | A | C | false | -1.439453 | -0.136844 | 0.141 | -0.007 | -0.002 | null |
1 | 1,211,917 | G | A | false | -0.191895 | -0.013032 | 0.135 | 0.028 | -0 | null |
1 | 1,212,042 | C | T | false | -3.046875 | -0.52087 | -0.003 | -3.889 | -0.003 | null |
1 | 1,212,898 | C | T | false | -0.602051 | -0.438368 | 0.235 | 4.258 | -0 | null |
1 | 1,232,800 | G | C | false | -1.115234 | -0.830179 | -0.466 | 1.097 | -0.998 | -2.994 |
1 | 1,243,102 | A | G | false | 5.085938 | -1.275063 | -2.096 | -5.327 | -0.99 | 3.157 |
1 | 1,243,545 | G | A | false | -7.59375 | -2.557367 | -7.839 | -6.608 | -1 | -9.774 |
1 | 1,264,812 | C | G | false | 4.078125 | -1.274881 | 0.188 | 0.183 | -0.719 | 0.67 |
1 | 1,285,621 | A | G | false | -1.320313 | -1.028294 | 1.673 | 0.04 | -0 | -2.734 |
1 | 1,288,005 | G | C | false | 3.164063 | -0.149565 | 0.07 | -3.204 | -0 | -1.253 |
1 | 1,291,377 | G | A | false | 0.023026 | -0.44613 | 0.087 | -1.21 | -0 | -4.715 |
1 | 1,291,509 | G | A | false | 0.664063 | 0.265035 | 2.719 | 4.19 | -0 | -4.258 |
1 | 1,319,063 | G | A | false | -0.026367 | 0.448394 | 2.002 | 0.861 | -0 | null |
1 | 1,332,271 | G | A | false | -0.956543 | 0.611933 | 2.457 | 4.275 | -0 | -3.367 |
1 | 1,334,108 | G | A | false | -0.147461 | -0.004351 | -0.198 | 1.406 | -0 | -6.573 |
1 | 1,420,203 | C | A | false | -1.3125 | -2.239272 | 1.246 | -0.527 | -0 | -10.381 |
1 | 1,426,261 | C | T | false | 1.09375 | -0.466194 | 0.724 | -0.952 | -0 | -1.575 |
1 | 1,452,384 | G | A | false | -4.957031 | -4.322648 | -8.17 | -8.528 | -1 | -13.144 |
1 | 1,495,605 | C | T | false | -1.003906 | -0.735766 | 0.688 | 0.039 | -0 | -4.705 |
1 | 1,512,312 | G | A | false | -5.585938 | -2.55411 | -3.349 | -8.396 | -0.999 | -3.698 |
1 | 1,517,186 | G | A | false | -1.466797 | -0.71163 | -1.385 | -2.202 | -0.011 | -4.841 |
1 | 1,616,547 | T | C | false | 1.503906 | -0.54761 | 0.394 | 0.175 | -0 | null |
1 | 1,640,423 | C | T | false | -4.613281 | -2.384015 | -5.637 | -3.468 | -0.995 | -7.286 |
1 | 1,641,819 | C | T | false | 0.884766 | -0.617502 | -0.039 | 0.278 | -0.987 | null |
1 | 1,668,373 | C | T | false | -3.203125 | -1.409952 | -3.753 | -2.372 | -0.998 | -5.63 |
1 | 1,668,449 | A | G | false | 0.150391 | 0.356083 | 0.521 | 3.961 | -0.048 | null |
1 | 1,707,486 | C | T | false | -2.923828 | -1.558467 | -3.757 | -6.882 | -0.998 | -10.252 |
1 | 1,707,555 | C | T | false | -3.8125 | -2.087687 | -4.923 | -3.468 | -0.984 | -7.325 |
1 | 1,719,406 | G | A | false | -1.825195 | -4.246027 | -6.251 | -5.87 | -1 | -7.366 |
1 | 1,754,601 | G | T | false | -6.25 | 0.4479 | 1.13 | 6.418 | -0.005 | -5.367 |
1 | 1,916,540 | T | C | false | 2.607422 | -1.204282 | 0.175 | 1.396 | -0 | 2.522 |
1 | 1,918,090 | A | G | false | -3.164063 | -0.828084 | -1.22 | -0.809 | -0.013 | -3.629 |
1 | 1,918,091 | T | C | false | -2.382813 | -0.067017 | 0.082 | 0.16 | -0.001 | -2.649 |
1 | 1,918,484 | C | A | false | -2.439453 | -0.529345 | 0.094 | 0.465 | -0.014 | -3.765 |
1 | 1,923,107 | C | T | false | -3.990234 | -2.031239 | -0.55 | -5.883 | -0.438 | -3.655 |
1 | 1,927,692 | C | T | false | 0.583008 | 1.649318 | 3.588 | 5.924 | -0 | -4.229 |
1 | 1,927,737 | T | C | false | 1.25293 | -0.435867 | 0.144 | -3.951 | -0 | -2.232 |
1 | 1,930,143 | C | T | false | -6.273438 | -3.552757 | -3.98 | -6.968 | -1 | -7.93 |
1 | 1,942,086 | T | C | false | 3.904297 | -1.532497 | -2.516 | -1.494 | -0.999 | -7.38 |
1 | 1,944,419 | C | G | false | -7.394531 | -2.364683 | -1.874 | -4.094 | -0.939 | -9.653 |
1 | 1,968,793 | T | C | false | 2.328125 | 0.478732 | -0.054 | -0.904 | -0.001 | -4.6 |
1 | 2,025,598 | T | C | false | 3.611328 | -1.082832 | 1.217 | -0.193 | -0 | null |
1 | 2,029,235 | C | T | false | -0.580078 | -0.219853 | 0.476 | 1.463 | -0.112 | null |
1 | 2,193,733 | G | A | false | -1.341797 | -0.285874 | 0.118 | -0.297 | -0 | -4.024 |
1 | 2,228,951 | C | G | false | -7.238281 | -2.898948 | -1.587 | -5.155 | -1 | -3.98 |
1 | 2,430,581 | G | T | false | -2.886719 | -0.784373 | -0.073 | 2.269 | -0 | null |
1 | 2,509,919 | T | C | false | 0.943359 | 0.013537 | 1.142 | 0.23 | -0 | -3.214 |
1 | 2,512,975 | G | A | false | -3.662109 | -1.970945 | -3.998 | -4.597 | -0.61 | -6.44 |
1 | 2,556,714 | A | G | false | -0.836426 | -0.451203 | 1.268 | 1.328 | -0 | -1.235 |
1 | 2,562,891 | G | A | false | -0.208008 | 0.730034 | 2.026 | 3.287 | -0 | -3.62 |
1 | 2,595,307 | A | G | false | 1.491211 | 1.702114 | 2.273 | 6.32 | -0 | -5.036 |
1 | 2,800,059 | C | T | false | -0.524414 | -0.216149 | -0.524 | -0.467 | -0 | null |
1 | 3,022,425 | G | A | false | -6.765625 | -3.676768 | -6.676 | -6.789 | -1 | -8.122 |
1 | 3,412,095 | C | T | false | -4.460938 | -2.384755 | -4.653 | -3.25 | -1 | -6.268 |
1 | 3,473,163 | C | T | false | -5.140625 | -1.426175 | -1.729 | -5.333 | -0.681 | -8.124 |
1 | 3,494,017 | G | A | false | -4.394531 | -0.033623 | -0.771 | -1.944 | -0 | -6.066 |
1 | 3,494,409 | C | T | false | -1.060547 | 1.078686 | 7.111 | 6.721 | -0 | -3.219 |
1 | 3,497,304 | C | G | false | -4.730469 | -1.726461 | -0.8 | -0.692 | -0.104 | -6.124 |
1 | 3,497,541 | C | T | false | -4.125 | -0.831787 | -2.746 | -2.785 | -0.76 | null |
1 | 3,505,333 | A | G | false | 1.557617 | -0.610779 | -1.398 | -0.862 | -0.004 | -0.87 |
1 | 3,507,824 | G | A | false | -3.925781 | -3.351424 | -5.604 | -3.236 | -1 | -7.972 |
1 | 3,512,044 | G | A | false | -3.664063 | -2.21538 | -5.734 | -2.223 | -0.979 | -6.956 |
1 | 3,595,370 | A | G | false | 3.074219 | -0.865236 | -0.757 | -1.86 | -0.468 | -1.141 |
1 | 3,752,641 | C | G | false | 1.786133 | 1.120535 | 1.373 | -0.218 | -0 | -4.008 |
1 | 3,761,369 | T | C | false | -0.373779 | 0.229329 | 0.597 | 1.925 | -0.531 | -2.061 |
1 | 3,763,211 | C | T | false | 0.558105 | 1.513619 | 4.489 | 4.443 | -0 | -4.287 |
1 | 3,763,322 | C | T | false | 0.021973 | 1.651928 | 6.568 | 0.769 | -0 | -2.834 |
1 | 3,829,360 | G | A | false | -2.253906 | -2.742005 | -2.135 | -2.347 | -1 | -7.244 |
1 | 3,836,572 | A | T | false | -3.042969 | 0.038535 | 0.286 | 1.467 | -0 | -4.647 |
1 | 3,843,220 | A | G | false | 0.765137 | -0.157686 | 0.506 | 0.272 | -0.001 | -2.372 |
1 | 3,860,425 | C | T | false | 2.324219 | -0.241725 | 0.637 | 0.804 | -0.068 | null |
1 | 3,869,681 | G | A | false | 2.746094 | -0.987071 | -2.446 | -1.729 | -1 | -4.199 |
1 | 3,890,558 | G | A | false | -0.515625 | 0.243785 | 1.877 | 0.909 | -0 | null |
1 | 3,891,607 | T | C | false | -0.232666 | 0.38678 | 2.356 | 7.718 | -0 | null |
1 | 3,892,762 | C | T | false | -1.25 | -0.172378 | 0.03 | -0.127 | -0 | null |
1 | 4,712,657 | G | A | false | -2.541016 | -2.179927 | -1.474 | -6.476 | -0.019 | -3.775 |
1 | 6,082,379 | C | T | false | -1.250977 | -0.622828 | -0.107 | -1.929 | -0 | null |
1 | 6,124,032 | A | G | false | 4.714844 | -1.830434 | -0.362 | -3.455 | -0.161 | -2.164 |
1 | 6,130,155 | C | T | false | -1.390625 | 0.132878 | 1.68 | 0.177 | -0 | null |
1 | 6,207,471 | C | T | false | -1.673828 | -1.781214 | -0.961 | -0.402 | -0.412 | -5.259 |
1 | 6,212,018 | G | A | false | 2.572266 | 0.537066 | -0.346 | 4.152 | -0.069 | -3.762 |
1 | 6,218,354 | A | G | false | 3.066406 | -0.075304 | 0.309 | -0.75 | -0 | -1.905 |
1 | 6,219,310 | G | C | false | -1.507813 | -0.028565 | 0.117 | -1.875 | -0 | -4.261 |
1 | 6,245,232 | C | A | false | -5.835938 | -0.960845 | -1.81 | -3.302 | -0.891 | -5.028 |
1 | 6,253,878 | C | T | false | -1.854492 | -0.18674 | 0.046 | 1.683 | -0.653 | -4.624 |
1 | 6,413,234 | A | G | false | 1.286133 | -0.446791 | -0.289 | -0.578 | -0.001 | -2.295 |
1 | 6,418,980 | G | A | false | -2.335938 | -0.509035 | 0.164 | -0.124 | -0.001 | -3.37 |
1 | 6,448,812 | C | T | false | -2.498047 | -1.356739 | 0.437 | -0.948 | -0 | -5.094 |
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COSMIC variants
For more information check out our paper and repository.
Usage
- Pandas
import pandas as pd
df = pd.read_parquet("hf://datasets/songlab/cosmic/test.parquet")
- Polars
import polars as pl
df = pl.read_parquet("https://huggingface.co/datasets/songlab/cosmic/resolve/main/test.parquet")
- Datasets
from datasets import load_dataset
dataset = load_dataset("songlab/cosmic", split="test")
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Size of the auto-converted Parquet files:
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Number of rows:
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