Debian 13 (Trixie) native package

r-bioc-genomicalignments

BioConductor representation and manipulation of short genomic alignments

Packages / Debian 13 (Trixie) / gnu-r / r-bioc-genomicalignments

Package: r-bioc-genomicalignments (1.42.0-2)

Maintainers:

Debian R Packages Maintainers

External Resources:

Homepage: [bioconductor.org]

BioConductor representation and manipulation of short genomic alignments

Other Packages Related to r-bioc-genomicalignments:

dep: r-api-4.0
Package not available
dep: r-api-bioc-3.20
Package not available
dep: [r-bioc-biocgenerics] (>= 0.37.0)
generic functions for Bioconductor
dep: [r-bioc-s4vectors] (>= 0.27.12)
BioConductor S4 implementation of vectors and lists
dep: [r-bioc-iranges] (>= 2.23.9)
GNU R low-level containers for storing sets of integer ranges
dep: [r-bioc-genomeinfodb] (>= 1.13.1)
BioConductor utilities for manipulating chromosome identifiers
dep: [r-bioc-genomicranges] (>= 1.55.3)
BioConductor representation and manipulation of genomic intervals
dep: [r-bioc-summarizedexperiment] (>= 1.9.13)
BioConductor assay container
dep: [r-bioc-biostrings] (>= 2.55.7)
GNU R string objects representing biological sequences
dep: [r-bioc-rsamtools] (>= 1.31.2)
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
dep: [r-bioc-biocparallel]
BioConductor facilities for parallel evaluation
dep: [libc6] (>= 2.4)
GNU C Library: Shared libraries

sug: [r-bioc-shortread]
GNU R classes and methods for high-throughput short-read sequencing data
sug: [r-bioc-rtracklayer]
GNU R interface to genome browsers and their annotation tracks
sug: [r-bioc-bsgenome]
BioConductor infrastructure for Biostrings-based genome data packages
sug: [r-bioc-genomicfeatures]
GNU R tools for making and manipulating transcript centric annotations
sug: [r-bioc-deseq2]
R package for RNA-Seq Differential Expression Analysis
sug: [r-bioc-edger]
Empirical analysis of digital gene expression data in R
sug: [r-cran-runit]
GNU R package providing unit testing framework
sug: [r-cran-knitr]
GNU R package for dynamic report generation using Literate Programming
sug: [r-bioc-biocstyle]
standard styles for vignettes and other Bioconductor documents

Download r-bioc-genomicalignments

Architecture	Package Size	Installed Size	Files
amd64	2.1 MiB	3.3 MiB	[list of files]
arm64	2.1 MiB	3.4 MiB	[list of files]

Package file paths (50)

Paths come from the repository package-file index for the observed builds. They describe archive/package associations, not every file that will exist on a running system after maintainer scripts, alternatives, generated state, diversions, or installation choices.

/usr/lib/R/site-library/GenomicAlignments/CITATION
/usr/lib/R/site-library/GenomicAlignments/DESCRIPTION
/usr/lib/R/site-library/GenomicAlignments/doc/GenomicAlignmentsIntroduction.pdf
/usr/lib/R/site-library/GenomicAlignments/doc/GenomicAlignmentsIntroduction.R
/usr/lib/R/site-library/GenomicAlignments/doc/GenomicAlignmentsIntroduction.Rnw
/usr/lib/R/site-library/GenomicAlignments/doc/index.html
/usr/lib/R/site-library/GenomicAlignments/doc/OverlapEncodings.pdf
/usr/lib/R/site-library/GenomicAlignments/doc/OverlapEncodings.R
/usr/lib/R/site-library/GenomicAlignments/doc/OverlapEncodings.Rnw
/usr/lib/R/site-library/GenomicAlignments/doc/summarizeOverlaps.pdf
/usr/lib/R/site-library/GenomicAlignments/doc/summarizeOverlaps.R
/usr/lib/R/site-library/GenomicAlignments/doc/summarizeOverlaps.Rnw
/usr/lib/R/site-library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.html
/usr/lib/R/site-library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.R
/usr/lib/R/site-library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.Rmd
/usr/lib/R/site-library/GenomicAlignments/extdata/sm_treated1.bam
/usr/lib/R/site-library/GenomicAlignments/extdata/sm_untreated1.bam
/usr/lib/R/site-library/GenomicAlignments/help/aliases.rds
/usr/lib/R/site-library/GenomicAlignments/help/AnIndex
/usr/lib/R/site-library/GenomicAlignments/help/GenomicAlignments.rdb
/usr/lib/R/site-library/GenomicAlignments/help/GenomicAlignments.rdx
/usr/lib/R/site-library/GenomicAlignments/help/paths.rds
/usr/lib/R/site-library/GenomicAlignments/html/00Index.html
/usr/lib/R/site-library/GenomicAlignments/html/R.css
/usr/lib/R/site-library/GenomicAlignments/INDEX
/usr/lib/R/site-library/GenomicAlignments/libs/GenomicAlignments.so
/usr/lib/R/site-library/GenomicAlignments/Meta/features.rds
/usr/lib/R/site-library/GenomicAlignments/Meta/hsearch.rds
/usr/lib/R/site-library/GenomicAlignments/Meta/links.rds
/usr/lib/R/site-library/GenomicAlignments/Meta/nsInfo.rds
/usr/lib/R/site-library/GenomicAlignments/Meta/package.rds
/usr/lib/R/site-library/GenomicAlignments/Meta/Rd.rds
/usr/lib/R/site-library/GenomicAlignments/Meta/vignette.rds
/usr/lib/R/site-library/GenomicAlignments/NAMESPACE
/usr/lib/R/site-library/GenomicAlignments/NEWS
/usr/lib/R/site-library/GenomicAlignments/R/GenomicAlignments
/usr/lib/R/site-library/GenomicAlignments/R/GenomicAlignments.rdb
/usr/lib/R/site-library/GenomicAlignments/R/GenomicAlignments.rdx
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_cigar-utils.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_coordinate-mapping-methods.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_findSpliceOverlaps-methods.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_GAlignments-class.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_GAlignmentsList-class.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_intra-range-methods.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_readGAlignmentPairs.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_readGAlignmentsList.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_readGAlignments.R
/usr/lib/R/site-library/GenomicAlignments/unitTests/test_summarizeOverlaps-methods.R
/usr/share/doc/r-bioc-genomicalignments/changelog.Debian.gz
/usr/share/doc/r-bioc-genomicalignments/copyright

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Use this package

OpenFactory can boot this operating system in a browser VM, or start a build that includes the native package name from this record.

Try Debian 13 (Trixie) in the browser Build an image that includes r-bioc-genomicalignments

Versions, suites, and repositories

Each row is recorded package-index metadata for one version, architecture, suite, and repository. Names, URLs, and sizes are source-reported; a link is a potentially mutable retrieval location, not an OpenFactory redistribution claim or proof that OpenFactory retained the artifact bytes.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
1.42.0-2	trixie / main	amd64	Debian 13 · main · amd64	2.1 MiB	3.3 MiB	pool/main/r/r-bioc-genomicalignments/r-bioc-genomicalignments_1.42.0-2_amd64.deb
1.42.0-2	trixie / main	arm64	Debian 13 · main · arm64	2.1 MiB	3.4 MiB	pool/main/r/r-bioc-genomicalignments/r-bioc-genomicalignments_1.42.0-2_arm64.deb

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Checksums and observation dates

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

1.42.0-2 / amd64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: ec544729027516e54ad41ed1a7cc8abbfec011249daf93b62a2a1b6bbc51282d

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' 'ec544729027516e54ad41ed1a7cc8abbfec011249daf93b62a2a1b6bbc51282d' 'r-bioc-genomicalignments_1.42.0-2_amd64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

1.42.0-2 / arm64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: 7be03f029e81f0590b0caaa97e0db640c4d9cac959959c57e9b308c86e34c3da

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' '7be03f029e81f0590b0caaa97e0db640c4d9cac959959c57e9b308c86e34c3da' 'r-bioc-genomicalignments_1.42.0-2_arm64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 13 (Trixie) main arm64 revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908

Catalog record completeness

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3, Debian 13 (Trixie) main arm64 revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and provenance

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 13 (Trixie) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/trixie/InRelease
Signed-object SHA-256
98b25b5cd185c59d34aa6e4c3e9b5b8f01bbe9d104fe2dcfbcd30dc0a14a59ed
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Observed SHA-256: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Result: match verified
Debian 13 (Trixie) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/trixie/InRelease
Signed-object SHA-256
98b25b5cd185c59d34aa6e4c3e9b5b8f01bbe9d104fe2dcfbcd30dc0a14a59ed
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Observed SHA-256: 753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Result: match verified