inst/README.md

In rodrigarc/RepertoiR: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Folder organization

Inside this folder there are 3 different subfolders:

• script

  • contains a text file describing in detail how the raw data present in extdata was generated

• rmd

  • contains Rmarkdown files that are used by quality_report() function to generate quality reports for all the sequences (HC_report.Rmd) and for individual reports for each sample (HC_individualized_report.Rmd)

• extdata

  • contains folders with raw data from single-cell sorted B cell receptor sanger sequencing (sorted_sangerseq) and flow cytometry data from when those cells were sorted (fcs_index_sorting)

    • fcs_index_sorting: .fcs files from one sample sorted in different plates. eg. E18_02 means sample E18, plate 02.

    • sorted_sangerseq: contains 2 folders for matching one of the samples in fcs_index_sorting.

      • E18_C1: contains raw .ab1 files from 12 wells sequenced by sanger sequencing
      • E18_C1_R: contains raw .ab1 files from 12 wells that were re-sequenced (repeated) to try to improve sequence quality

rodrigarc/RepertoiR documentation built on June 15, 2024, 7:16 p.m.