| Deposited data |
|
| Raw and analyzed data |
https://data.humancellatlas.org/explore/projects/cc95ff89-2e68-4a08-a234-480eca21ce79?catalog=dcp1 |
Census of Immune Cells |
| Raw and analyzed data |
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE134355&format=file |
GSE134355 |
| Raw and analyzed data |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118546;
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118852
|
GSE118480 |
| Raw and analyzed data |
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE96583 |
GSE96583 |
|
| Software and algorithms |
|
| Scanpy (v1.6.0) |
(Wolf et al., 2018)39
|
https://github.com/theislab/scanpy |
| Pegasus (v1.4.3) |
(Bo Li el at., 2020) |
https://github.com/lilab-bcb/pegasus |
| scVI(v0.6.8) |
(Lopez et al., 2018)8
|
https://github.com/theislab/scvelo |
| MNN (v1.8.0) |
(Laleh Haghverdi et al.,2018)28
|
https://github.com/MarioniLab/MNN2017 |
| Combat (v1.8.0) |
(Jean-Philippe Fortin et al.,2017) |
https://github.com/Jfortin1/ComBatHarmonization |
| Harmony (v0.1.6) |
(Ilya Korsunsky et al., 2019)29
|
https://github.com/immunogenomics/harmony |
| Seurat (v3.1.5) |
(Butler et al., 2018)30
|
https://satijalab.org/seurat |
| Scanorama (v1.7.1) |
(Brian Hie el al.,2019)33
|
https://github.com/brianhie/scanorama |
| DESC (v2.1.1) |
(Xiangjie Li et at., 2020)37
|
https://eleozzr.github.io/desc/ |
| iMAP (v1.0.0) |
(Dongfang Wang et at., 2021)36
|
https://github.com/Svvord/iMAP |
| scArches (v 1.7.0) |
(Mohammad Lotfollahi et al., 2021)35
|
https://github.com/theislab/scarches |
| BBKNN (v 1.7.1) |
(Krzysztof Polański et al., 2020)32
|
https://github.com/Teichlab/bbknn |
| tGPT |
(Hongru Shen et al., 2023) |
https://github.com/deeplearningplus/tGPT |
