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Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells

Year: 2024

Type: article

Abstract: Here you will find all the data, code, and analysis used for the scifer manuscript. scifer is an R/Bioconductor package that can preprocess raw data from index sorts and raw BCR Sanger sequencing data. It can identify high-quality sequences based on different parameters, such as length, Phred scores, and heavy-chain complementarity-determining region 3 (HCDR3) quality. As a result, it significantly increases the quality of germline assignments and reduces spurious variable gene mutations. Its output provides quality control reports, FASTA files, summarized tables, and electropherograms for manual inspection.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.8399140

Authors: Arcoverde Cerveira, Rodrigo, Lenart, Klara, Martin, Marcel, Hinchcliff, Matthew James, Hellgren, Fredrika, Yu, Kewei, Assis Geraldo, Juliana, Kreslavsky, Taras, Ols, Sebastian, Loré, Karin

Institutions: Karolinska University Hospital, Karolinska Institutet, National Bioinformatics Infrastructure Sweden

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W4387295331

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