api reference#
read and write: io
#
Read and integrate the ouput data produced by 10x Genomics’ CellRanger,
load and save integrated AnnData
objects to h5ad
-formatted files, and concatenate
multiple AnnData
objects.
Tip
All of the methods in io
are also available directly from scab
itself,
so scab.read_10x_mtx()
is identical to scab.io.read_10x_mtx()
. This was
done to make the API more consistent with scanpy.
Each function is designed to replicate the behavior of their scanpy or anndata equivalent, but
to add necessary fuctionality to accomodate BCR and/or TCR sequence data. For example, BCR/TCR
annotations cannot be writted to h5ad
-formatted files, so scab.save()
will serialize them prior
to saving, and de-serialize when loading with scab.load()
.
Reads 10x Genomics data into an integrated |
|
Loads a serialized |
|
Serializes and saves an |
|
Concatenates |
preprocessing: pp
#
Filtering and normalization of GEX data, doublet detection and removal.
performs quality filtering and normalization of 10x Genomics count data |
|
Removes doublets. |
|
Predicts doublets using scrublet [Wolock19]. |
|
Predicts doublets using doubletdetection [Gayoso20]. |
tools: tl
#
Filtering and normalization of GEX data, doublet detection and removal.
batch correction#
Batch effect correction using ComBat [Johnson07]. |
|
Data integration and batch correction using mutual nearest neighbors [Haghverdi19]. |
|
Data integration and batch correction using mutual nearest neighbors [Haghverdi19]. |
|
cell hashes#
Demultiplexes cells using cell hashes. |
clonality#
Assigns BCR sequences to clonal lineages using the clonify [Briney16] algorithm. |
embeddings#
specificity#
Classifies BCR specificity using antigen barcodes (AgBCs). |