diff --git a/docs/RESULTS-DOCUMENTATION.md b/docs/RESULTS-DOCUMENTATION.md index 5362a9a..29ae6e1 100644 --- a/docs/RESULTS-DOCUMENTATION.md +++ b/docs/RESULTS-DOCUMENTATION.md @@ -166,6 +166,14 @@ You can define microenvironments with prior knowledge, imaging or Visium analysi # Input files +## Data format advice + +NOTE Please _do not use_ the following in any of your input (e.g. Counts and Meta) files: + +> Numeric cell type names (see [GitHub issue #148](https://github.com/ventolab/CellphoneDB/issues/148)) + +> Dashes ("-") in cell names (see [GitHub issue #144](https://github.com/ventolab/CellphoneDB/issues/144))) + ## Counts file For large datasets, do not use .txt files to input counts `test_counts.txt`. Please, input counts as h5ad (recommended), h5 or a path to a folder containing a 10x output with mtx/barcode/features files. @@ -178,6 +186,7 @@ For large datasets, do not use .txt files to input counts `test_counts.txt`. Ple This is the file linking bacodes/cells to clusters/cell types. This file is generated by the users after they have annotated each cluster identified by scRNA-seq data (e.g., by using packages such as Seurat and SCANPY). The file contains two columns: ‘Cell’, indicating the name of the cell; and ‘cell_type’, indicating the name of the cluster considered. Formats accepted are .csv, .txt, .tsv, .tab and .pickle. + ## DEGs file This file is only used by is METHOD 3 `degs_analysis`. It is a .txt with two columns: the first column should be the cell type name and the second column the associated significant gene id. The remaining columns are ignored. See example [here](https://github.com/ventolab/CellphoneDB/blob/master/in/endometrium_atlas_example/endometrium_example_DEGs.tsv).