Package: sangerseqR 1.43.0

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_1.43.0.tar.gz
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sangerseqR_1.43.0.tgz(r-4.4-any)sangerseqR_1.43.0.tgz(r-4.3-any)
sangerseqR_1.43.0.tar.gz(r-4.5-noble)sangerseqR_1.43.0.tar.gz(r-4.4-noble)
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sangerseqR.pdf |sangerseqR.html✨
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-1.43.0(bioc 3.21)sangerseqR-1.42.0(bioc 3.20)

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

sequencing snp visualization

6.10 score 2 packages 62 scripts 1.4k downloads 8 mentions 22 exports 48 dependencies

Last updated 23 days agofrom:1d424d9a83. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

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:askpass base64enc BiocGenerics Biostrings bslib cachem cli commonmark crayon curl digest fastmap fontawesome fs GenomeInfoDb GenomeInfoDbData glue htmltools httpuv httr IRanges jquerylib jsonlite later lifecycle magrittr memoise mime openssl promises pwalign R6 rappdirs Rcpp rlang S4Vectors sass shiny sourcetools stringi stringr sys UCSC.utils vctrs withr xtable XVector zlibbioc

Using the sangerseqR package

Jonathon T. Hill, PhD

Rendered fromsangerseqRWalkthrough.Rmdusingknitr::rmarkdownon Oct 31 2024.

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