Package: QuasR 1.45.1

Michael Stadler

QuasR: Quantify and Annotate Short Reads in R

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Authors:Anita Lerch [aut], Adam Alexander Thil SMITH [aut], Charlotte Soneson [aut], Dimos Gaidatzis [aut], Michael Stadler [aut, cre]

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NEWS

# Install 'QuasR' in R:

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

Bug tracker:https://github.com/fmicompbio/quasr/issues

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:QuasR-1.45.1(bioc 3.20)QuasR-1.44.0(bioc 3.19)

bioconductor-package

13 exports 1.75 score 108 dependencies 1 dependents 30 mentions

Last updated 2 months agofrom:16f5555bbd

Exports:alignments alignmentStats auxiliaries genome preprocessReads qAlign qCount qExportWig qMeth qProfile qProjectUpdate qQCReport show

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray deldir digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges glue hms httr httr2 hwriter interp IRanges jpeg jsonlite KEGGREST lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr pwalign R6 rappdirs Rbowtie RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors ShortRead snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 VariantAnnotation vctrs withr XML xml2 XVector yaml zlibbioc

An introduction to QuasR

Michael Stadler, Dimos Gaidatzis, Charlotte Soneson, Anita Lerch

Rendered fromQuasR.Rmdusingknitr::rmarkdownon Jun 18 2024.

Last update: 2024-03-14
Started: 2018-01-05

Help page	Topics
Get statistics on alignments	alignmentStats
Preprocess Short Reads	preprocessReads
Align reads	qAlign
Quantify alignments	qCount
QuasR wig file export	qExportWig
Quantify DNA methylation	qMeth
Quantify alignments by relative position	qProfile
qProject objects	alignments alignments,qProject-method auxiliaries auxiliaries,qProject-method class:qProject genome,qProject-method length,qProject-method qProject qProject-class show,qProject-method [,qProject,ANY,missing,missing-method
Update qProject	qProjectUpdate
QuasR Quality Control Report	qQCReport

Package: QuasR 1.45.1

QuasR: Quantify and Annotate Short Reads in R

An introduction to QuasR

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)