Package: sangerseqR 1.49.0

Jonathon Hill

sangerseqR: Tools for Sanger Sequencing Data in R

This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

Authors:Jonathon T. Hill, Bradley Demarest

sangerseqR_1.49.0.tar.gz
sangerseqR_1.49.0.zip(r-4.7)sangerseqR_1.49.0.zip(r-4.6)sangerseqR_1.49.0.zip(r-4.5)
sangerseqR_1.49.0.tgz(r-4.6-any)sangerseqR_1.49.0.tgz(r-4.5-any)
sangerseqR_1.49.0.tar.gz(r-4.7-any)sangerseqR_1.49.0.tar.gz(r-4.6-any)
sangerseqR_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
sangerseqR/json (API)

# Install 'sangerseqR' in R:

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

On BioConductor:sangerseqR-1.49.0(bioc 3.24)sangerseqR-1.48.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing snp visualization

5.96 score 2 packages 96 scripts 8 mentions 22 exports 42 dependencies

Last updated from:d6784281be. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	146
linux-devel-x86_64	NOTE	254
source / vignettes	OK	206
linux-release-x86_64	NOTE	260
macos-release-arm64	NOTE	128
macos-oldrel-arm64	NOTE	121
windows-devel	NOTE	153
windows-release	NOTE	145
windows-oldrel	NOTE	151
wasm-release	OK	147

Exports:chromatogram makeBaseCalls peakAmpMatrix peakAmpMatrix<-peakPosMatrix peakPosMatrix<-PolyPeakParser primarySeq primarySeq<-primarySeqID primarySeqID<-read.abif read.scf readsangerseq sangerseq secondarySeq secondarySeq<-secondarySeqID secondarySeqID<-setAllelePhase traceMatrix traceMatrix<-

Dependencies:base64enc BiocGenerics Biostrings bslib cachem cli commonmark crayon digest fastmap fontawesome fs generics glue htmltools httpuv IRanges jquerylib jsonlite later lifecycle magrittr memoise mime otel promises pwalign R6 rappdirs Rcpp rlang S4Vectors sass Seqinfo shiny sourcetools stringi stringr vctrs withr xtable XVector

Using the sangerseqR package

Rendered fromsangerseqRWalkthrough.Rmdusingknitr::rmarkdown

Last update: 2023-03-08
Started: 2023-03-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for Sanger Sequencing Data in R	sangerseqR-package sangerseqR
ABIF Class Objects	abif abif-class
Generate Chromatogram	chromatogram chromatogram,sangerseq-method
Make Basecalls	makeBaseCalls makeBaseCalls,sangerseq-method
Run Poly Peak Parser	PolyPeakParser
Sangerseq Accessor Functions	peakAmpMatrix peakAmpMatrix,sangerseq-method peakAmpMatrix<- peakAmpMatrix<-,sangerseq-method peakPosMatrix peakPosMatrix,sangerseq-method peakPosMatrix<- peakPosMatrix<-,sangerseq-method primarySeq primarySeq,sangerseq-method primarySeq<- primarySeq<-,sangerseq-method primarySeqID primarySeqID,sangerseq-method primarySeqID<- primarySeqID<-,sangerseq-method secondarySeq secondarySeq,sangerseq-method secondarySeq<- secondarySeq<-,sangerseq-method secondarySeqID secondarySeqID,sangerseq-method secondarySeqID<- secondarySeqID<-,sangerseq-method traceMatrix traceMatrix,sangerseq-method traceMatrix<- traceMatrix<-,sangerseq-method
Read ABIF Files	read.abif
Read Scf Files	read.scf
Read Scf or ABIF Files	readsangerseq
Sangerseq Class Objects	sangerseq sangerseq,abif-method sangerseq,scf-method sangerseq-class
Scf Class Objects	scf scf-class
Set Reference and Alternate Alleles	setAllelePhase setAllelePhase,sangerseq-method