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crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis

Gonzalo Soria-Alcaide1,2, Gonzalo García-Aguilera1, Marta Portasany-Rodríguez1,2

  • 1Fundación para la Investigación Biomédica Hospital Infantil Universitario Niño Jesús (FIBHNJS), Madrid, Spain.

BMC Genomics
|March 22, 2026
PubMed
Abstract

No abstract available in PubMed .

Keywords:
BCRClonotypeImmune repertoireImmunologyPipelineTCRscRNAseq

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CRISPR and crRNAs02:53

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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