Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
were remapped with cellranger vdj and processed further using Dandelion as described above. For all samples, contigs were extracted from ‘all_contig_igblast_db-all.tsv’ or in the case whereby ‘all_contig_igblast_db-all.tsv’ was empty, ‘all_contig_igblast_db-fail.tsv’ was used. Preprocessed and annotated scRNA-seq data was downloaded from. Only contigs from annotated cells were kept for downstream analysis.
Raw scRNA-seq reads were mapped with cellranger 3.0.2 with Ensembl 93-based GRCh38 reference. Low-quality cells were filtered out (minimum number of reads >2,000, minimum number of genes >500, maximum number of genes <7,000, maximum mitochondrial reads fraction <0.2 and maximum scrublet
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