Input data format

Expression data for two different species for comparison is required. For each of these species provide the input gene expression data is expected in one of the following formats:

1. Spreadsheet of comma-separated values csv where rows are genes, columns are cells with gene expression counts, this should be accompanied by another dataframe with two columns with one specifying batches and the other specifying corresponding cells. Alternatively, the first row of the dataframe should be 'batch' and the second 'cell'.

Cell vs Genes	Batches and Cells
cell C1 C2 C3 C4 G1 3 1 7 G2 2 2 2 G3 3 1 5 G4 10 5 4 … … … … …	batch cell B1 C1 B1 C2 B2 C3 B3 C4 … …

or:

batch	batch0	batch0	batch1	batch1
cell	C1	C2	C3	C4
G1		3	1	7
G2	2	2		2
G3	3	1		5
G4	10		5	4
…	…	…	…	…

2. Pandas DataFrame where axis 0 is genes and axis 1 are cells. If the are batched in the data then the index of axis 1 should have two levels, e.g. ('batch', 'cell'), with the first level indicating patient, batch or expreriment where that cell was sequenced, and the second level containing cell barcodes for identification.

df = pd.DataFrame(data=[[2,np.nan],[3,8],[3,5],[np.nan,1]],
                  index=['G1','G2','G3','G4'],
                  columns=pd.MultiIndex.from_arrays([['batch0','batch1'],['C1','C2']], names=['batch', 'cell']))