Contains loom files and preprocessed adata objects to compare methods for temporal gene expression integration. Loom files can be accessed using the 'read' function in Scvelo. Preprocessed adata objects can be accessed using the 'read_h5ad' function in Scanpy. The raw single-cell RNA sequencing datasets can be found under the following accession codes. Mouse embryonic cell cycle dataset from Ref. (https://doi.org/10.1038/nbt.3102) was originally downloaded from ArrayExpress with the accession code E-MTAB-2805 Hematopoiesis differentiation dataset from Ref. (https://doi.org/10.1182/blood-2016-05-716480) was originally downloaded from the Gene Expression Omnibus with the accession code GSE81682 NKT cell differentiation dataset from Ref. (https://doi.org/10.1038/ni.3437) was originally downloaded from the Gene Expression Omnibus with the accession code GSE74596. Hematopoiesis differentiation dataset from Ref. (https://doi.org/10.1038/nature19348) was originally downloaded from the Gene Expression Omnibus with the accession codes GSE70236, GSE70240, GSE70244 LPS stimulation dataset from Ref. (https://doi.org/10.1016/j.cels.2017.03.010) was originally downloaded from the Gene Expression Omnibus with the accession code GSE94383. INF-gamma stimulation dataset from Ref. (https://doi.org/10.1038/s41587-020-00803-5) was originally downloaded from the Gene Expression Omnibus with the accession code GSE161465. AML chemotherapy dataset from Ref. (https://doi.org/10.1038/s41591-018-0233-1) was originally downloaded from the Gene Expression Omnibus with the accession code GSE116481. AML diagnosis/relapse dataset from Ref. (https://doi.org/10.1038/s41375-021-01338-7) was originally downloaded from the Gene Expression Omnibus with the accession code GSE126068. MS case control PBMC and CSF datasets from Ref. (https://doi.org/10.1038/s41467-019-14118-w) was originally downloaded from the Gene Expression Omnibus with the accession code GSE138266.