Package: scifer 1.7.3

Rodrigo Arcoverde Cerveira

scifer: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, 'fasta' files, electropherograms for visual inspection, and generate reports.

Authors:Rodrigo Arcoverde Cerveira [aut, cre, cph], Sebastian Ols [aut, dtc], Karin Loré [dtc, ths]

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NEWS

# Install 'scifer' in R:

install.packages('scifer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rodrigarc/scifer/issues

On BioConductor:scifer-1.7.1(bioc 3.20)scifer-1.6.0(bioc 3.19)

bioconductor-package

8 exports 0.71 score 106 dependencies

Last updated 6 days agofrom:a11fe5e3d4

Exports:df_to_fasta fcs_plot fcs_processing igblast quality_report secondary_peaks summarise_abi_file summarise_quality

Dependencies:askpass base64enc basilisk basilisk.utils BH Biobase BiocGenerics Biostrings bslib cachem cli colorspace commonmark cpp11 crayon curl cytolib data.table DBI DECIPHER digest dir.expiry dplyr evaluate fansi farver fastmap filelock flowCore fontawesome fs generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gridExtra gtable here highr htmltools httpuv httr IRanges isoband jquerylib jsonlite kableExtra knitr labeling later lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plyr png promises pwalign R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate Rhdf5lib rlang rmarkdown rprojroot RProtoBufLib rstudioapi S4Vectors sangerseqR sass scales shiny sourcetools stringi stringr svglite sys systemfonts tibble tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun xml2 xtable XVector yaml zlibbioc

Using scifer to filter single-cell sorted B cell receptor (BCR) sanger sequences

Rodrigo Arcoverde Cerveira

Rendered fromscifer_walkthrough.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2022-09-08
Started: 2022-09-06

Help page	Topics
Fasta file creation from dataframe columns and/or vectors.	df_to_fasta
Plot flow data from index sorted cells	fcs_plot
Extract index sorting information from flow cytometry data	fcs_processing
Run IgDiscover for IgBlast using basilisk, which enables the python environment for Igblast	igblast
Generate general and individualized reports	quality_report
Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences	scifer
Check for secondary peaks in a sangerseq object	secondary_peaks
Create a summary of a single ABI sequencing file	summarise_abi_file
Generate a summary table containing quality measurements from sanger sequencing abi files	summarise_quality

Package: scifer 1.7.3

scifer: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Using scifer to filter single-cell sorted B cell receptor (BCR) sanger sequences

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