Package: BamScale 0.99.10

Chirag Parsania

BamScale: Bioconductor-Friendly Multithreaded BAM Processing

Multithreaded sequential BAM processing built on top of the ompBAM C++ engine. BamScale provides user-friendly BAM read and scan interfaces designed for compatibility with existing Bioconductor workflows.

Authors:Chirag Parsania [aut, cre]

BamScale_0.99.10.tar.gz
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BamScale_0.99.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BamScale/json (API)

# Install 'BamScale' in R:
install.packages('BamScale', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cparsania/bamscale/issues

Pkgdown/docs site:https://cparsania.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:BamScale-0.99.10(bioc 3.24)

softwaredataimportsequencingcoveragealignmentqualitycontrolcpp

4.90 score 85 downloads 5 exports 35 dependencies

Last updated from:026ff90e05. Checks:1 NOTE, 13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE218
linux-devel-arm64OK215
linux-devel-x86_64OK262
source / vignettesOK288
linux-release-arm64OK216
linux-release-x86_64OK283
macos-release-arm64OK105
macos-release-x86_64OK246
macos-oldrel-arm64OK110
macos-oldrel-x86_64OK340
windows-develOK209
windows-releaseOK221
windows-oldrelOK211
wasm-releaseOK214

Exports:bam_countbam_readdecode_compact_qualdecode_compact_seqdecode_seqqual_compact

Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarillocodetoolscpp11crayonDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsompBAMRcppRhtslibRsamtoolsS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentXVector

Getting started with BamScale
Introduction | Installation | Basic usage | Metadata-oriented BAM access | Filtering with ScanBamParam | Alignment-object output | Sequence and quality extraction | Fast count summaries | Relationship to existing Bioconductor tools | Session information
Rendered fromBamScale-intro.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2026-04-20

Benchmarking BamScale Across Step1, GAlignments, and SeqQual Workloads
Overview | Data Loading | Benchmark Provenance | Methods Rationale | Input Files | Reference Counts | Best-Observed Summary | BamScale-versus-Comparator Fold Change | Single-File step1 | Single-File galignments | Multi-File step1 | Multi-File galignments | Single-File seqqual | Multi-File seqqual | Compact-versus-Compatible seqqual | Interpretation | Session Information
Rendered frombenchmark-results.Rmdusingknitr::rmarkdown

Last update: 2026-04-20
Started: 2026-04-20