Parallel version of hECA data with batch-correction
| Title | Parallel version of hECA data with batch-correction |
|---|---|
| Description | Considering some users may prefer to be able to download data that have been processed with more batch-correction processing, we did a series of comparison experiments on the popular methods, and chose to use the Harmony method (Korsunsky et al., 2019). Harmony is one of the most used integration methods but it does not provide the corrected matrix. We added an extra step upon the standard Harmony method to calculate the corrected expression matrix from the vectors in the corrected embedding space with the inverse-transformation. We had experimented with multiple methods for cross-organ batch-effect correction but none of them worked well since there are no shared cell types across some organs. Therefore, we applied the extended Harmony method on cells of the same organ, and do this batch-effect correction separately for each organ. We provided the data thus processed as a parallel version of the hECA data for each organ here. |
| Organism | Homo |
| Data Type | - |
| Data Accessibility | Open-access |
| BioProject | PRJCA008680 |
| Release Date | 2022-03-17 |
| Submitter | Yixin Chen (chenyx19@mails.tsinghua.edu.cn) |
| Organization | Tsinghua University |
| Submission Date | 2022-03-16 |
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| File ID | File Title | Number/Samples | File Type | File Size | File Suffix | Download Times | Download |
|---|---|---|---|---|---|---|---|
| OMIX001042-20-01 | Ilem dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 296.01 MB | corrected.rds | 0 | |
| OMIX001042-20-02 | Adipose dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 265.01 MB | corrected.rds | 0 | |
| OMIX001042-20-03 | Adrenal gland dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.72 GB | corrected.rds | 0 | |
| OMIX001042-20-04 | Bladder dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 160.92 MB | corrected.rds | 0 | |
| OMIX001042-20-05 | Adult blood dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.38 GB | Adult.corrected.rds | 0 | |
| OMIX001042-20-06 | Fetal blood dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.12 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-07 | Bone marrow dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.09 GB | corrected.rds | 0 | |
| OMIX001042-20-08 | Adult brain dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.39 GB | Adult.corrected.rds | 0 | |
| OMIX001042-20-09 | Fetal brain dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 9.34 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-10 | Bronchi dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.15 GB | corrected.rds | 0 | |
| OMIX001042-20-11 | Colon dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.27 GB | corrected.rds | 0 | |
| OMIX001042-20-12 | Duodenum dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 331.28 MB | corrected.rds | 0 | |
| OMIX001042-20-13 | Adult eye dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 7.33 GB | adult.corrected.rds | 0 | |
| OMIX001042-20-14 | Fetal eye dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.32 MB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-15 | Gallbladder dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.07 GB | corrected.rds | 0 | |
| OMIX001042-20-16 | Adult heart dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 43.89 GB | Adult.corrected.rds | 0 | |
| OMIX001042-20-17 | Fetal heart dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.78 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-18 | Adult Intestine dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.63 GB | Adult.corrected.rds | 0 | |
| OMIX001042-20-19 | Fetal Intestine dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.68 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-20 | Jejunum dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 562.96 MB | corrected.rds | 0 | |
| OMIX001042-20-21 | Adult kidney dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.85 GB | Adult.corrected.rds | 0 | |
| OMIX001042-20-22 | Fetal kidney dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.47 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-23 | Liver dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 8.08 GB | corrected.rds | 0 | |
| OMIX001042-20-24 | Adult lung dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 541.76 MB | Adult.corrected.rds | 0 | |
| OMIX001042-20-25 | Fetal lung dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 32.38 MB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-26 | Oesophagus dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 13.54 GB | corrected.rds | 0 | |
| OMIX001042-20-27 | Ovary dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 906.96 MB | corrected.rds | 0 | |
| OMIX001042-20-28 | Fetal pancreas dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.42 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-29 | Plancenta dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.41 GB | corrected.rds | 0 | |
| OMIX001042-20-30 | Pleura dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 6.05 GB | corrected.rds | 0 | |
| OMIX001042-20-31 | Rectum dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.06 GB | corrected.rds | 0 | |
| OMIX001042-20-32 | Rib dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.31 GB | corrected.rds | 0 | |
| OMIX001042-20-33 | Skin dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 853.2 MB | corrected.rds | 0 | |
| OMIX001042-20-34 | Spinal cord dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.06 GB | corrected.rds | 0 | |
| OMIX001042-20-35 | Spleen dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.82 GB | corrected.rds | 0 | |
| OMIX001042-20-36 | Adult stomach dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.12 GB | Adult.corrected.rds | 0 | |
| OMIX001042-20-37 | Fetal stomach dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.09 GB | Fetal.corrected.rds | 0 | |
| OMIX001042-20-38 | Testis dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 1.86 GB | corrected.rds | 0 | |
| OMIX001042-20-39 | Thymus dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 517.34 MB | corrected.rds | 0 | |
| OMIX001042-20-40 | Thyroid dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 3.29 GB | corrected.rds | 0 | |
| OMIX001042-20-41 | Ureter dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 125.3 MB | corrected.rds | 0 | |
| OMIX001042-20-42 | Vessel dataset with batch-correction in hECA v1.0 | 1 | Transcriptomic | 2.81 GB | corrected.rds | 0 |