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Error code: DatasetGenerationError Exception: CastError Message: Couldn't cast input_ids: list<item: int32> child 0, item: int32 cell_types: string organ_major: string disease: string length: int64 -- schema metadata -- huggingface: '{"info": {"features": {"input_ids": {"feature": {"dtype": "' + 255 to {'input_ids': Sequence(feature=Value(dtype='int32', id=None), length=-1, id=None), 'cell_type': Value(dtype='string', id=None), 'organ_major': Value(dtype='string', id=None), 'length': Value(dtype='int64', id=None)} because column names don't match Traceback: Traceback (most recent call last): File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1997, in _prepare_split_single for _, table in generator: File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 688, in wrapped for item in generator(*args, **kwargs): File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/arrow/arrow.py", line 67, in _generate_tables yield f"{file_idx}_{batch_idx}", self._cast_table(pa_table) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/arrow/arrow.py", line 55, in _cast_table pa_table = table_cast(pa_table, self.info.features.arrow_schema) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2302, in table_cast return cast_table_to_schema(table, schema) File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema raise CastError( datasets.table.CastError: Couldn't cast input_ids: list<item: int32> child 0, item: int32 cell_types: string organ_major: string disease: string length: int64 -- schema metadata -- huggingface: '{"info": {"features": {"input_ids": {"feature": {"dtype": "' + 255 to {'input_ids': Sequence(feature=Value(dtype='int32', id=None), length=-1, id=None), 'cell_type': Value(dtype='string', id=None), 'organ_major': Value(dtype='string', id=None), 'length': Value(dtype='int64', id=None)} because column names don't match The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1391, in compute_config_parquet_and_info_response parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet( File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 990, in stream_convert_to_parquet builder._prepare_split( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1884, in _prepare_split for job_id, done, content in self._prepare_split_single( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2040, in _prepare_split_single raise DatasetGenerationError("An error occurred while generating the dataset") from e datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset
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input_ids
sequence | cell_type
string | organ_major
string | length
int64 |
---|---|---|---|
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131,
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2522,
20426,
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1785,
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223,
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11819,
6712,
2205,
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15308,
7928,
3897,
9581,
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10046,
37,
7424,
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14122,
174,
13516,
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6725,
10346,
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11223,
10352,
1548,
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730,
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3989,
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11847,
2348,
12084,
8579,
8734,
7630,
17975,
17308,
7085,
15529,
21359,
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12049,
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14520,
8470,
10690,
4225,
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11172,
5092,
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16393,
5710,
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35662,
17979,
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2438,
17031,
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172,
8210,
2719,
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6963,
3471,
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15214,
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11228,
4468,
17740,
6170,
11267,
1569,
9770,
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1192,
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15542,
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2599,
4171,
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16875,
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15119,
1802,
55809,
21003,
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3618,
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731,
19062,
16030,
231,
17149,
14630,
5288,
13554,
10858,
654,
14368,
647
] | mature NK T cell | EX_breast | 1,183 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 807 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,075 |
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6937,
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21047,
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1711,
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12428,
976,
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12075,
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19953,
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5592,
458,
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15243,
2343,
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18949,
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11247,
17943,
3316,
2367,
16445,
6825,
19481,
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17635,
14881,
5729,
3694,
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1245,
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3658,
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2710,
17839,
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6920,
16416,
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12195,
17887,
10851,
10011,
8799,
485,
22821,
1582,
8414,
17962,
11569,
1452,
16067,
10424,
4471,
5629,
4408,
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3664,
2717,
5130,
7884,
3026,
6859,
11215,
13433,
7006,
16185,
12658,
7764,
10691,
9917,
15000,
3797,
16518,
2689,
2579,
2522,
2080,
5150,
5514,
7484,
12363,
20484,
11056,
3679,
3683,
9795,
2379,
328,
1908,
8067,
12299,
32990,
4507,
3538,
1578,
17283,
2503,
1955,
330,
2542,
10949,
5378,
8698,
1421,
8936,
15263,
17304,
2100,
4602,
9212,
14680,
5745,
1225,
8670,
4687,
2175,
4954,
6116,
6494,
1358,
9443,
5107,
633,
9147,
11080,
9181,
7942,
2683,
5213,
3725,
10830,
28446,
6818,
17745,
8429,
5867,
130,
7274,
21049,
859,
480,
4811,
7125,
8006,
1656,
4563,
12615,
3021,
2619,
17369,
14380,
487,
2146,
3171,
3176,
20828,
904,
14698,
12817,
944,
11145,
7600,
8120,
560,
7033,
6565,
2571,
3674,
9343,
4707,
8994,
8717,
11697,
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16735,
3847,
2243,
3641,
6325,
2482,
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22739,
10915,
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686,
14803,
7579,
1489,
7337,
1556,
31051,
12057,
3383,
10343,
20152,
16536,
7143,
22685,
12614,
16025,
7387,
12432,
12186,
6665,
15695,
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15107,
5368,
5088,
14042,
11747,
15888,
2690,
5427,
7911,
8316,
15534,
7635,
10977,
2450,
1992,
22524,
5065,
13347,
12651,
14163,
6058,
15463,
16030,
4374,
1199,
2950,
3382,
2030,
9039,
378,
2520,
1881,
973,
11143,
3833,
10218,
2928,
6810,
16114,
6158,
3995,
1981,
10432,
8213,
16618,
7382,
16603,
6629,
8776,
5058,
3898,
1690,
14122,
318,
13516,
7765,
19415,
3409,
17936,
3757,
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3665,
10352,
1535,
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17030,
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2991,
9260,
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1805,
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1354,
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6520,
17137,
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12672,
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31835,
7414,
4224,
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21003,
2463,
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127,
9084,
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2627,
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53,
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7613,
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9026,
1904,
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5203,
780,
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276,
7280,
9814,
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4300,
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4442,
11975,
12294,
15936,
7440,
6836,
5708,
3058,
9744,
4898,
22481,
9214,
1946,
6062,
2596,
5748,
3032,
3620,
11470,
2331,
4601,
1524,
1927,
16039,
798,
4298,
16628,
11082,
11450,
8063,
15344,
12258,
2380,
1730,
6723,
530,
2002,
35677,
17530,
35548,
16576,
2214,
9288,
3607,
8187,
571,
14602,
8340,
1941,
2552,
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13586,
2259,
17170,
52,
3220,
33,
1720,
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1976,
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3434,
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11438,
7266,
16697,
1802,
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17990,
28222,
327,
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129,
5790,
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20208,
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791,
4979,
13554,
2298,
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2034,
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5006,
17007,
4612,
17567,
20088,
3588,
17987,
2699,
12392,
8419,
14556,
20011,
16651
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,176 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 723 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 821 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 727 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,338 |
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5526,
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16378,
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5203
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 890 |
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17962,
5721,
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1802,
9022,
654,
4612
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 593 |
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31102,
8310,
15554,
6198,
13257,
6667,
11794,
8716,
1594,
6922,
8774,
5295,
4004,
2231,
23025,
6739,
21326,
6397,
3434,
8038,
11438,
16697,
16030,
19036,
2423,
1188,
28222,
327,
14636,
17962,
17990,
11260,
16494,
137,
2939,
4267,
12945,
13554,
20757,
6572,
11336,
12258,
14630,
3542,
31707,
10367,
9904,
17184,
1283,
12388,
17119,
20088,
5203,
20574,
8775,
13697,
36947,
17972,
976,
4796,
9854,
5092,
17689,
6381,
585,
13433,
1413,
9022,
21601,
2321,
8408,
7414,
9788,
20208,
10858,
5442,
8003,
17981,
11067,
2476,
17978,
31412,
31356,
17402,
32123,
5439,
13358,
4590,
22962,
3220,
654,
1741,
6937,
17162,
13184,
5721,
129,
14876,
17979,
17975,
6487,
16636,
8289,
1187,
31051,
10837,
1703,
11118,
19062,
11369,
231,
174,
15400,
14556,
1802,
17100,
4979,
16638,
17641,
4610,
16490,
14069,
17983,
17397,
16988,
2699,
19204,
16809,
17287,
1186,
12117,
2298,
6990,
7838,
17848,
17255,
1399,
13688,
17567,
1140,
16758,
13940,
17745,
6724,
12392,
4612,
16651,
17007
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 504 |
[
2535,
22916,
10606,
17353,
17490,
2002,
15826,
10285,
5045,
115,
3334,
4361,
2034,
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177,
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15554,
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3129,
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2173,
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2701,
2115,
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1842,
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28160,
51740,
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2254,
6264,
14397,
11837,
5820,
8504,
1764,
5161,
14777,
7948,
8960,
3139,
16925,
16011,
12624,
3513,
9501,
11067,
1020,
621,
14025,
6237,
8253,
13068,
3316,
6470,
14936,
1897,
12802,
3842,
17397,
11909,
7368,
6168,
11453,
5227,
11219,
19204,
11244,
3128,
4902,
7150,
19481,
27883,
13845,
9579,
17684,
6176,
4875,
12254,
10075,
2476,
6352,
1316,
6481,
1996,
3694,
2292,
9787,
15734,
6416,
11471,
13827,
15672,
2209,
9464,
13433,
13688,
22860,
14932,
13284,
1188,
4442,
12294,
2162,
5497,
15831,
4761,
17224,
4061,
6101,
1283,
1946,
3032,
2331,
1524,
17966,
1927,
16128,
12675,
3811,
15344,
17119,
31051,
13940,
10440,
29164,
7283,
12654,
66,
2552,
8150,
16871,
16494,
31869,
16372,
2086,
12769,
6394,
2320,
2228,
20117,
8195,
6003,
11305,
3940,
334,
1829,
284,
7663,
10988,
20963,
5324,
15049,
14069,
15149,
12117,
14556,
6487,
13358,
17981,
9966,
14184,
8571,
982,
1622,
32071,
15736,
8289,
576,
1187,
9747,
8674,
10769,
5803,
11913,
4170,
7284,
11149,
5254,
1133,
7659,
1711,
10773,
6643,
15453,
5322,
5529,
17287,
4140,
7414,
12392,
15747,
8294,
14131,
637,
15700,
16363,
5006,
8040,
8902,
17745,
14796,
9612,
9129,
8836,
11436,
4590,
17972,
32123,
3267,
16327,
5784,
17962,
14079,
4088,
662,
3230,
1484,
3825,
14793,
129,
7687,
1332,
11469,
15438,
9975,
19183,
8938,
2935,
10954,
6274,
14368,
1703,
11118,
3075,
4021,
16651,
20029,
19062,
1713,
3955,
17379,
3618,
7327,
10335,
3027,
21794,
19668,
1741,
6990,
8310,
23025,
10658,
4378,
36947,
13184,
17983,
15273,
17149,
16638,
17975,
14876,
654,
6922,
8839,
14630,
5442,
6739,
6475,
4017,
19900,
17990,
451,
16697,
19036,
3993,
16378,
1413,
2298,
11831,
11260,
17111,
17007,
6819,
2939,
19841,
10367,
2699,
3516,
9172,
3542,
17100,
17567,
4612,
215,
8419,
1166,
1908,
2417,
4979,
3589,
6810,
17979,
17978,
19360,
9759,
5721,
8590,
14655,
3148,
2104,
16758,
21047,
15301,
7720,
12568,
31404,
3017,
17987,
5288,
5526,
17848,
585,
20011,
647
] | mature NK T cell | EX_breast | 894 |
[
2535,
10606,
88,
6079,
10810,
10024,
853,
730,
22624,
2900,
15715,
1122,
9751,
19649,
9233,
4875,
15734,
3371,
17490,
17353,
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8560,
5790,
26823,
31905,
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20565,
6667,
21320,
19265,
17430,
20817,
55,
1255,
7964,
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9327,
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2841,
5864,
20491,
470,
20836,
5314,
8306,
12307,
5485,
5763,
12062,
5986,
4773,
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8638,
14390,
10851,
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3289,
706,
933,
1277,
10199,
8986,
12430,
13277,
3078,
6267,
774,
4505,
10483,
3136,
10896,
9660,
2592,
14086,
4151,
10826,
12834,
1955,
5271,
6948,
9458,
14027,
1647,
10444,
11165,
9181,
7718,
11873,
6869,
16123,
15377,
7371,
1983,
506,
9089,
1745,
19953,
2104,
16007,
14281,
560,
5249,
6216,
14291,
4707,
6474,
6974,
3946,
4942,
15702,
10943,
6984,
4884,
22861,
20152,
1105,
15160,
2796,
1691,
14733,
9182,
11645,
1447,
9643,
5733,
11341,
13348,
1199,
16429,
5323,
2847,
8803,
2954,
11143,
22071,
3301,
7928,
1791,
14845,
6608,
19499,
8335,
9762,
4999,
630,
3244,
10078,
10513,
3320,
9260,
12501,
1962,
20391,
15529,
15551,
8616,
21092,
6675,
6486,
20143,
16708,
12868,
10491,
8747,
728,
5282,
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6409,
4789,
9125,
2985,
2719,
16186,
2886,
14638,
1940,
4515,
3356,
7203,
19917,
14633,
11669,
7392,
20612,
12044,
17676,
11500,
12289,
5509,
7784,
10640,
11347,
16330,
7945,
17286,
2046,
6529,
7587,
437,
31421,
668,
2295,
19417,
2147,
11134,
13197,
31264,
3439,
7078,
8868,
19062,
433,
9331,
5586,
6950,
6695,
13843,
3261,
3826,
20991,
636,
6500,
15208,
8681,
10285,
17752,
20574,
10616,
3448,
1468,
8666,
19335,
10357,
17126,
10507,
5765,
18949,
9500,
21378,
11580,
8524,
9930,
2706,
1190,
11892,
266,
16707,
6943,
1180,
17246,
3190,
1710,
3482,
6185,
2937,
48303,
12945,
54784,
22820,
13932,
11214,
14846,
5941,
29190,
7788,
20551,
1964,
8949,
10162,
15311,
13988,
8775,
5606,
10867,
5245,
10220,
9992,
7368,
4975,
2034,
1059,
19481,
4040,
3915,
20490,
9814,
8677,
7912,
10383,
6416,
115,
10105,
14045,
1073,
80,
6360,
22460,
11196,
422,
3184,
2102,
11545,
7623,
3032,
13166,
530,
3860,
1773,
9309,
14230,
16372,
12007,
6032,
4540,
11305,
3660,
11717,
284,
20566,
10451,
1247,
16790,
8357,
9202,
6235,
4206,
4441,
19779,
16665,
3091,
5366,
19782,
12160,
5519,
1711,
16267,
1897,
10,
10907,
4078,
1632,
9349,
258,
4140,
10580,
3148,
6352,
13293,
17147,
4591,
11412,
3699,
519,
8212,
12075,
3267,
7979,
1484,
3825,
15966,
11921,
1332,
15890,
18942,
1086,
12428,
1558,
10954,
4301,
2524,
4358,
22530,
3955,
7628,
22916,
7327,
10335,
177,
13433,
6581,
17712,
11826,
20757,
16378,
6990,
7036,
6919,
15273,
16741,
1976,
13688,
1048,
17641,
31356,
4004,
13697,
12153,
3434,
8038,
11438,
10075,
16030,
16697,
231,
12258,
16636,
2423,
1166,
15400,
11831,
327,
7682,
6819,
13554,
4267,
4610,
10367,
14630,
31707,
12388,
11478,
1399,
9854,
976,
32071,
32123,
17689,
15018,
6229,
6381,
585,
3017,
6810,
1413,
31051,
17745,
6724,
1857,
7414,
17162,
8590,
11369,
19204,
1020,
14655,
12117,
17119,
3486,
13940,
16490,
14636,
4590,
5092,
654,
3220,
16758,
15243,
21047,
5442,
17990,
8289,
11067,
11794,
1188,
31412,
982,
11336,
17975,
1186,
11118,
731,
1187,
17287,
17397,
6572,
10858,
13184,
16988,
7393,
17402,
174,
17100,
4979,
23025,
16809,
13358,
17981,
20088,
12392,
14069,
6487,
1802,
10769,
5288,
17184,
2298,
17979,
1741,
17978,
5721,
5526,
14876,
17983,
9904,
129,
8003,
22962,
16638,
16651,
14368,
1283,
17007,
5203,
1140,
17972,
17966,
14556,
7838,
10837
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 527 |
[
2535,
10606,
12075,
80,
12449,
1255,
1642,
6430,
3405,
5323,
8505,
12553,
12796,
1507,
1570,
17126,
4247,
7131,
2730,
8524,
9186,
7420,
22916,
1059,
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15734,
10407,
5433,
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9214,
13002,
31707,
17465,
523,
17353,
10462,
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17296,
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329,
10606,
1127,
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31250,
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359,
21794,
115,
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12700,
6047,
445,
7201,
302,
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 627 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 656 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 967 |
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4358,
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1269,
6323,
1206,
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11668,
2509,
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31640,
10658,
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16278,
15554,
6919,
4610,
20565,
1976,
8716,
1594,
5295,
5625,
12153,
6475,
5680,
2710,
4017,
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31412,
11300,
451,
32071,
17893,
3421,
19036,
2423,
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7718,
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4612,
4267,
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7237,
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9564,
4975,
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10355,
1866,
12318,
2417,
6229,
6381,
17007,
5526,
34614,
1247,
6079,
10769,
21601,
5203,
10,
6176,
2104,
1413,
5439,
4301,
2034,
5006,
7720,
7036,
16327,
16450,
14368,
19062,
174,
647,
2298,
3017,
5721,
17255
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,082 |
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11913,
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22816,
17795,
16267,
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1127,
6937,
8244,
1413,
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9025,
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14131,
13184,
33210,
6300,
6990,
4301,
15700,
17119,
17162,
8212,
3816,
8902,
32071,
12229,
7621,
9612,
2327,
11110,
1187,
7118,
7427,
8836,
11436,
23025,
16629,
31777,
12050,
3399,
7456,
2296,
11921,
9955,
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5207,
14368,
31356,
20008,
17966,
13371,
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607,
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32123,
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6198,
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6572,
1186,
17983,
10858,
17745,
3511,
8774,
2231,
5625,
1399,
15965,
16494,
4017,
36947,
17972,
11300,
17981,
14630,
11336,
16651,
19036,
654,
16809,
4590,
585,
11260,
5442,
7682,
8003,
12289,
19841,
17979,
17987,
1906,
2699,
11478,
982,
11463,
976,
1866,
17689,
17397,
5203,
17567,
8419,
3589,
1166,
19200,
16988,
1140,
1857,
21601,
2321,
13940,
9788,
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2180,
14655,
1632,
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174,
7838,
17149,
3017,
17990,
4979,
5288,
215,
17255,
31051,
5006,
16638,
17007
] | mature NK T cell | EX_breast | 833 |
[
674,
2535,
5509,
22916,
424,
2034,
11438,
17490,
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15696,
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288,
10942,
34065,
9624,
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36947,
16638,
17287,
16651
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 777 |
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10837,
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17567,
2298,
12392
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 605 |
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3693,
11325,
11013,
3363,
6474,
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19628,
10578,
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1707,
2063,
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6984,
3383,
8095,
1934,
10343,
14630,
10168,
13376,
13535,
5453,
14484,
9348,
7007,
20570,
6665,
454,
33203,
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16867,
7413,
17416,
6987,
4399,
16436,
5168,
6760,
462,
3820,
2642,
9989,
7911,
19903,
14506,
11283,
2560,
45182,
11249,
8202,
10465,
14535,
4678,
17114,
4963,
12448,
6751,
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3101,
2847,
248,
378,
8915,
34065,
5962,
12031,
15455,
10005,
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20208,
3833,
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11819,
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290,
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318,
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2221,
14031,
28070,
19320,
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17730,
2464,
5030,
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5518,
1904,
3962,
2390,
11263,
1496,
54418,
1710,
1682,
42123,
53748,
8057,
1970,
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530,
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5727,
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1941,
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1086,
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11004,
2935,
6274,
4756,
17475,
21310,
4021,
585,
20029,
22530,
3955,
3618,
7327,
871,
5815,
3027,
15553,
5578,
11468,
6581,
4378,
17007,
9111,
11826,
6198,
647,
16741,
1976,
4475,
10631,
6922,
8774,
3180,
5295,
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5421,
3017,
6739,
12153,
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3434,
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11831,
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1166,
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31707,
9564,
4272,
1741,
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1866,
3001,
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1857,
9788,
1897,
2180,
10,
1632,
791,
5439,
12428,
15301,
2034,
7720,
32071,
17987,
5526
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,296 |
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7414,
31412,
11336,
17567,
5092,
5442,
16651
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 912 |
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3220,
4301,
7720,
20011,
2298,
17978,
16327,
17981,
5006,
12392,
654,
31404,
8959,
17007,
3588,
17966,
17962,
17975,
8419,
19200,
5721,
17255
] | CD4-positive, alpha-beta T cell | EX_breast | 787 |
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9524,
8078,
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1985,
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6983,
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14513,
8522,
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19054,
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6701,
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3994,
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17630,
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1738,
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11639,
3120,
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3029,
8835,
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2428,
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5950,
8885,
16428,
20157,
6468,
12422,
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11093,
4434,
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6245,
8182,
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8499,
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4944,
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12312,
1955,
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5831,
6534,
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3329,
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8280,
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,680 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,474 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,687 |
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802,
34614,
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21601,
2642,
6352,
2104,
791,
5509,
2034,
2298,
8959
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,912 |
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7748,
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6301,
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12348,
13353,
4784,
4208,
10901,
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19609,
2938,
8096,
13851,
1932,
11111,
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,707 |
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2003,
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4112,
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11082,
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1866,
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2417,
15018,
4899,
21601,
8590,
3486,
3148,
2104,
791,
6937,
15301,
8959
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,625 |
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,699 |
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9827,
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21601,
22470,
4838,
578,
3866,
10949,
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4593,
5386,
10394,
4266,
2534,
11733,
6212,
15905,
11595,
4220,
12071,
11251,
12367,
7492,
3770,
10700,
10254,
17962,
837,
1748,
4421,
11080,
7537,
3575,
8882,
7914,
8956,
8969,
974,
5544,
12990,
14500,
3036,
357,
6281,
6596,
12648,
9614,
32843,
17412,
10777,
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17044,
13159,
12069,
12089,
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15413,
4315,
1859,
2146,
2625,
16019,
12539,
4747,
18981,
1637,
10564,
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20169,
14281,
16007,
7292,
8564,
15848,
9918,
15964,
2105,
8103,
2564,
3997,
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1841,
11325,
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3674,
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3329,
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3549,
3597,
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4026,
4194,
8320,
71,
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1333,
3405,
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197,
1872,
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3946,
15050,
9143,
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2793,
1347,
12945,
2855,
4704,
3039,
11624,
319,
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4686,
2739,
11094,
16536,
8900,
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1317,
3034,
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33203,
5571,
1917,
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5619,
7508,
30830,
3430,
6987,
3238,
8086,
1691,
3820,
438,
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20148,
7580,
5427,
15534,
6552,
4112,
4457,
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17850,
11523,
19408,
10210,
16422,
10434,
16490,
12259,
4544,
20208,
3837,
4708,
7845,
2994,
16508,
13347,
8992,
19623,
3237,
4000,
1746,
17184,
2065,
14679,
9521,
5323,
1897,
9777,
34065,
4705,
10005,
2180,
32189,
11143,
20532,
6163,
6155,
16570,
10218,
11318,
10202,
3995,
9539,
2297,
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31438,
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3278,
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22526,
6076,
14119,
13958,
5109,
8437,
12640,
3989,
10513,
5937,
15005,
31133,
8977,
2754,
5749,
19929,
11847,
12084,
10702,
5582,
5592,
8594,
3415,
13994,
3486,
2064,
5471,
8605,
17137,
1201,
11999,
12672,
7034,
5117,
1441,
2874,
841,
9527,
14740,
11337,
11658,
4905,
20011,
16567,
948,
9218,
14840,
728,
3734,
591,
11941,
3569,
501,
10656,
4576,
1779,
11410,
16566,
8933,
8227,
15094,
753,
10127,
19038,
3394,
4330,
11905,
1540,
5687,
8374,
4248,
11316,
7072,
1940,
1102,
19701,
4520,
3356,
1192,
6366,
3685,
7203,
5900,
14633,
7421,
3850,
7593,
1137,
7585,
4635,
17730,
11434,
35560,
6077,
4726,
8818,
3379,
7347,
7042,
2858,
805,
5933,
11043,
1911,
3062,
5310,
8954,
3886,
2926,
8544,
4589,
5369,
2484,
15303,
469,
11746,
4797,
3249,
2232,
10375,
2104,
15766,
10853,
16636,
522,
6529,
12553,
4716,
3447,
11638,
22786,
3909,
15224,
8137,
8648,
6263,
9979,
21552,
563,
668,
4357,
7187,
18982,
3901,
3175,
2147,
15432,
5255,
15242,
2032,
3456,
8660,
835,
13197,
11329,
6236,
6452,
1458,
17762,
8480,
243,
4124,
6808,
3333,
6061,
1072,
12240,
5116,
13952,
9221,
5871,
2337,
11232,
6490,
15138,
2268,
3807,
4612,
9331,
14030,
4360,
211,
3119,
9020,
1018,
11605,
14629,
4090,
70,
12631,
31020,
11394,
14367,
12695,
9324,
9936,
4454,
8286,
953,
40692,
1507,
776,
7962,
6695,
2092,
13394,
23034,
16365,
14876,
5240,
4397,
20994,
10659,
10476,
3826,
6306,
3129,
28055,
9677,
16128,
10300,
2262,
702,
31043,
2393,
2307,
2056,
5662,
7831,
1570,
1754,
1401,
20347,
9481,
5462,
13799,
646,
2900,
2553,
12904,
9105,
6684,
1896,
7740,
12555,
5409,
3107,
3798,
12795,
396,
15715,
17611,
12822,
2183,
14555,
2883,
14503,
2409,
15670,
748,
407,
10056,
12136,
7168,
19498,
9426,
11067,
55657,
21376,
4247,
14050,
6891,
9728,
2336,
7003,
9531,
6905,
11580,
6791,
9388,
9961,
6457,
11157,
9569,
12630,
4878,
17041,
8111,
31119,
6943,
20712,
20120,
3387,
6402,
2219,
41270,
2475,
8389,
6868,
1481,
14508,
8496,
17719,
4491,
11263,
1496,
7716,
10485,
275,
13662,
12209,
12657,
6670,
1539,
22820,
5161,
4453,
6119,
2575,
566,
9761,
136,
7948,
16011,
12624,
6261,
910,
13736,
7788,
3291,
7420,
5589,
1964,
5261,
8253,
15228,
11377,
10582,
15968,
34199,
3943,
15221,
4639,
10162,
15311,
4760,
10119,
2621,
9773,
738,
5606,
3842,
3647,
9992,
3960,
11453,
7368,
4506,
2943,
9668,
17082,
5821,
12395,
56061,
1059,
8439,
7150,
19481,
16220,
606,
12254,
3705,
5716,
7197,
7280,
4047,
14226,
8677,
2753,
7912,
8935,
4300,
30964,
14881,
1996,
22826,
17402,
12356,
9787,
10383,
11471,
4795,
7950,
16446,
6704,
17352,
4721,
22718,
15629,
19542,
13284,
6835,
80,
5755,
7440,
15301,
1413,
22460,
12577,
3507,
4061,
19150,
12270,
18959,
10643,
9214,
15100,
11018,
5927,
7714,
10674,
9267,
2331,
4571,
21547,
10994,
31610,
13166,
2960,
4298,
11450,
13002,
2380,
6723,
530,
2002,
2511,
10440,
2214,
20746,
9288,
22577,
2139,
5410,
12063,
8187,
571,
66,
19845,
17465,
16871,
1773,
5873,
2806,
19016,
11736,
31869,
10024,
9309,
1674,
16372,
2086,
5225,
12769,
523,
5432,
6394,
102,
12007,
2320,
2924,
6924,
20117,
17490,
17353,
3940,
334,
3809,
1036,
11717,
9756,
7169,
20963,
5324,
3605,
10451,
8777,
5994,
7415,
1176,
16327,
9966,
6182,
3138,
5551,
12040,
4303,
9202,
6533,
15062,
3755,
8976,
8580,
3013,
21705,
1131,
19219,
2780,
1497,
8246,
7120,
3889,
5366,
5803,
12478,
10606,
19782,
3578,
7284,
11149,
3245,
15502,
1711,
16267,
10773,
7886,
6100,
5322,
9623,
11932,
8003,
4140,
15747,
853,
3351,
6300,
1283,
17147,
6990,
5297,
15700,
33179,
8040,
519,
9854,
3011,
10171,
10820,
2327,
7118,
7427,
10086,
11436,
17748,
14708,
16629,
16758,
1585,
5784,
14079,
12050,
10705,
3399,
3825,
26823,
3825,
2296,
15966,
9146,
11921,
7687,
5207,
4998,
13371,
8418,
15890,
6774,
10362,
18942,
1086,
9291,
19183,
16816,
17056,
17475,
382,
12303,
1802,
4358,
1713,
3955,
7628,
3723,
17379,
5815,
1206,
15810,
9086,
5610,
11668,
15553,
2509,
10367,
11468,
9111,
3587,
6919,
2191,
20565,
16586,
8716,
1594,
6922,
8774,
3588,
17100,
21326,
19204,
8556,
16697,
5288,
17641,
30748,
19036,
654,
11609,
8419,
12289,
7237,
31356,
31707,
10320,
9564,
15366,
10355,
15643,
2417,
15018,
1857,
8408,
2298,
1632,
6176,
3148,
791,
5439,
3220,
4301,
7720,
16494,
9975,
647,
3017,
13433
] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,557 |
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2535,
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9214,
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8212,
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28222,
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9955,
10075,
19062,
8737,
297,
10,
15890,
17979,
9291,
537,
6176,
3689,
17990,
10954,
31707,
31095,
12568,
21310,
14876,
5203,
9904,
3706,
16755,
22530,
14032,
3955,
3723,
16202,
11428,
871,
13025,
10011,
12783,
3166,
8186,
5808,
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5392,
13375,
16636,
12168,
11567,
12144,
52901,
340,
7304,
14448,
2683,
22637,
4436,
4723,
2431,
21049,
6175,
7634,
9007,
4561,
694,
9354,
7672,
16952,
10915,
2175,
6984,
11094,
22861,
6937,
13376,
4175,
17330,
5571,
3587,
15243,
1283,
5110,
3637,
17962,
11341,
4652,
4445,
223,
2847,
248,
19138,
6947,
1537,
8776,
6608,
37,
10346,
9337,
7310,
12544,
5752,
5749,
10710,
12365,
30738,
1976,
2933,
10367,
22598,
3589,
2344,
10642,
20757,
17978,
14541,
8545,
2566,
5140,
3494,
14658,
9022,
10802,
7103,
10900,
12028,
7196,
4698,
4828,
3728,
4357,
4694,
1950,
16846,
22783,
9934,
4536,
3738,
14446,
902,
5566,
174,
12695,
9324,
2092,
9677,
9616,
14324,
673,
5076,
12617,
12904,
17752,
2235,
6628,
21326,
1399,
32123,
1857,
6110,
20777,
15164,
10586,
253,
8880,
287,
10962,
5518,
1475,
5342,
3190,
31127,
28160,
1186,
1627,
9788,
13257,
11067,
6264,
16697,
14397,
7548,
3652,
7036,
16988,
17975,
6119,
11214,
1020,
16327,
4937,
621,
1964,
14655,
14069,
16314,
7572,
30748,
7698,
17966,
12395,
6953,
14556,
7150,
585,
6733,
4829,
1187,
5691,
3271,
14226,
5023,
1996,
13433,
17972,
2699,
10105,
36794,
6724,
22718,
8848,
10878,
4442,
6074,
5755,
9975,
327,
1877,
9744,
2121,
6278,
13261,
19646,
17981,
31412,
1946,
5748,
11470,
2960,
17397,
7682,
5439,
2214,
5727,
12289,
2939,
7235,
19016,
1741,
31869,
1674,
3849,
6394,
10837,
1300,
3660,
10462,
9845,
10988,
5324,
9889,
21254,
10451,
19204,
4808,
7930,
3138,
10882,
5551,
16638,
12040,
12428,
5092,
2347,
17296,
4303,
20011,
4391,
4441,
6487,
7953,
4590,
2780,
16665,
15736,
1188,
11478,
17745,
5510,
19782,
3578,
1133,
9854,
17158,
22816,
7538,
16267,
16809,
2865,
17162,
6340,
15747,
499,
11336,
36947,
5898,
4796,
10580,
13293,
13697,
5297,
15643,
115,
16363,
33179,
13940,
11369,
23025,
519,
3011,
6990,
14368,
14630,
7621,
5442,
9129,
31356,
17402,
17287,
11898,
2020,
2374,
1661,
129,
13184,
3267,
14079,
7414,
4088,
662,
647,
17184,
5207,
13371,
5006,
10362,
19200,
18942,
6079,
8938,
2935,
4979,
17475,
16758,
17641,
382,
17571,
6736,
12117,
16030,
4778,
7628,
7393,
3618,
17712,
12945,
6298,
16490,
3148,
14636,
1269,
5815,
10335,
6323,
1206,
12392,
15810,
9086,
8003,
17007,
7443,
17100,
31102,
1413,
7838,
10658,
31051,
5526,
11826,
5288,
17848,
1802,
6919,
4612,
13688,
12258,
6667,
5479,
10769,
13358,
8716,
3220,
3511,
1594,
17567,
16494,
16651,
5355,
6739,
8289,
21047,
6397,
5680,
12679,
20088,
19900,
11300,
17893,
8949,
20574,
22962,
177,
19036,
3993,
11609,
3588,
4267,
19841,
17119,
14019,
13715,
9564,
1140,
31404,
231,
2505,
10706,
1166,
1908,
724,
19360,
10435,
7277,
4737,
4946,
2755,
2764,
2892,
8113,
16423,
14174,
7981,
12541,
9447,
19458,
11992,
19176,
16397,
2481,
423,
12313,
8697,
11827,
1789,
7071,
19396,
2531,
12189,
15381,
9909,
24,
8875,
12479,
5413,
16940,
20603,
7991,
12762,
5981,
21010,
10043,
12397,
3709,
15562,
13993,
2712,
2925,
5443,
1858,
12468,
6145,
10904,
6238,
19512,
11114,
10958,
684,
812,
7536,
17339,
3486,
4922,
22702,
15498,
241,
316,
9785,
16881,
11562,
4769,
135,
3376,
2284,
1381,
759,
9158,
8878,
2834,
12746,
10799,
14284,
3919,
17171,
30855,
5720,
19022,
5220,
14158,
16001,
6233,
12699,
16470,
6512,
2963,
5105,
6000,
2658,
17375,
19511,
1392,
11345,
8625,
8728,
10979,
7047,
11758,
13459,
15577,
5157,
13328,
551,
15612,
7468,
8822,
1619,
1348,
15447,
2098,
8414,
8151,
15121,
17630,
12098,
220,
15827,
13486,
8654,
9491,
4781,
6255,
8267,
9783,
13896,
552,
4324,
9350,
706,
11153,
1837,
16902,
10382,
654,
4692,
2275,
4588,
16650,
9405,
6605,
2897,
2011,
3089,
7006,
6277,
17878,
8096,
166,
6798,
2673,
11395,
18984,
5232,
6267,
12327,
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] | effector memory CD8-positive, alpha-beta T cell | EX_breast | 1,666 |
Mouse-Genecorpus-20M
Write: Keita Ito
Abstract
This repository contains the datasets of mouse-Genecorpus-20M and evaluation datasets to analysis. Mouse-Genecorpus-20M is large-scale pretraining corpus comprised of ~21 million mosue single cell transcriptomes from a broad range of tissues from publicly available data. This corpus is used for pretraining mouse-Geneformer, a pretrained transformer model that enables context-aware predictions in settings with limited data in network biology.
[bioRxiv]
Citation
If you find this repository is useful. Please cite the following references.
@article{Ito2024.09.09.611960,
author = {Ito, Keita and Hirakawa, Tsubasa and Shigenobu, Shuji and Fujiyoshi, Hironobu and Yamashita, Takayoshi},
title = {Mouse-Geneformer: A Deep Leaning Model for Mouse Single-Cell Transcriptome and Its Cross-Species Utility},
journal = {bioRxiv},
year = {2024},
URL = {https://www.biorxiv.org/content/early/2024/09/13/2024.09.09.611960}
}
How to use
You need to download datasets on your disk you want to use. After doing, you program in python as follow to use its :
from datasets inport load_from_disk
dataset = load_from_disk("/path/to/mouse-Genecorpus-20M/MLM-re_All_mouse_tokenize_dataset.dataset/")
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