Debian 13 (Trixie) native package

r-bioc-shortread

GNU R classes and methods for high-throughput short-read sequencing data

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

Package: r-bioc-shortread (1.64.0-3)

Maintainers:

Debian R Packages Maintainers

External Resources:

Homepage: [bioconductor.org]

GNU R classes and methods for high-throughput short-read sequencing data

Other Packages Related to r-bioc-shortread:

dep: r-api-4.0
Package not available
dep: r-api-bioc-3.20
Package not available
dep: [r-bioc-biocgenerics] (>= 0.23.3)
generic functions for Bioconductor
dep: [r-bioc-biocparallel]
BioConductor facilities for parallel evaluation
dep: [r-bioc-biostrings] (>= 2.47.6)
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-genomicalignments] (>= 1.15.6)
BioConductor representation and manipulation of short genomic alignments
dep: [r-bioc-biobase]
base functions for Bioconductor
dep: [r-bioc-s4vectors] (>= 0.17.25)
BioConductor S4 implementation of vectors and lists
dep: [r-bioc-iranges] (>= 2.13.12)
GNU R low-level containers for storing sets of integer ranges
dep: [r-bioc-genomeinfodb] (>= 1.15.2)
BioConductor utilities for manipulating chromosome identifiers
dep: [r-bioc-genomicranges] (>= 1.31.8)
BioConductor representation and manipulation of genomic intervals
dep: [r-bioc-pwalign]
Perform pairwise sequence alignments
dep: [r-cran-hwriter]
HTML Writer - Outputs R objects in HTML format
dep: [r-cran-lattice]
GNU R package for 'Trellis' graphics
dep: [r-cran-latticeextra]
GNU R package of additional graphical displays based on lattice
dep: [r-bioc-xvector]
BioConductor representation and manpulation of external sequences
dep: [r-bioc-rhtslib]
HTSlib high-throughput sequencing library as GNU R package
dep: [libc6] (>= 2.14)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libstdc++6] (>= 11)
GNU Standard C++ Library v3
dep: [zlib1g] (>= 1:1.1.4)
compression library - runtime

sug: [r-bioc-biocstyle]
standard styles for vignettes and other Bioconductor documents
sug: [r-cran-runit]
GNU R package providing unit testing framework
sug: [r-bioc-biomart]
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
sug: [r-bioc-genomicfeatures]
GNU R tools for making and manipulating transcript centric annotations
sug: [r-cran-knitr]
GNU R package for dynamic report generation using Literate Programming

Download r-bioc-shortread

Architecture	Package Size	Installed Size	Files
amd64	5.0 MiB	8.0 MiB	[list of files]
arm64	5.0 MiB	8.1 MiB	[list of files]

Package file paths (112)

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/ShortRead/CITATION
/usr/lib/R/site-library/ShortRead/DESCRIPTION
/usr/lib/R/site-library/ShortRead/doc/index.html
/usr/lib/R/site-library/ShortRead/doc/Overview.html
/usr/lib/R/site-library/ShortRead/doc/Overview.R
/usr/lib/R/site-library/ShortRead/doc/Overview.Rmd
/usr/lib/R/site-library/ShortRead/extdata/bowtie/s_1_aligned_bowtie.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
/usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
/usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
/usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
/usr/lib/R/site-library/ShortRead/extdata/maq/out.aln.1.txt
/usr/lib/R/site-library/ShortRead/extdata/maq/out.aln.2.txt
/usr/lib/R/site-library/ShortRead/help/aliases.rds
/usr/lib/R/site-library/ShortRead/help/AnIndex
/usr/lib/R/site-library/ShortRead/help/paths.rds
/usr/lib/R/site-library/ShortRead/help/ShortRead.rdb
/usr/lib/R/site-library/ShortRead/help/ShortRead.rdx
/usr/lib/R/site-library/ShortRead/html/00Index.html
/usr/lib/R/site-library/ShortRead/html/R.css
/usr/lib/R/site-library/ShortRead/INDEX
/usr/lib/R/site-library/ShortRead/libs/ShortRead.so
/usr/lib/R/site-library/ShortRead/Meta/features.rds
/usr/lib/R/site-library/ShortRead/Meta/hsearch.rds
/usr/lib/R/site-library/ShortRead/Meta/links.rds
/usr/lib/R/site-library/ShortRead/Meta/nsInfo.rds
/usr/lib/R/site-library/ShortRead/Meta/package.rds
/usr/lib/R/site-library/ShortRead/Meta/Rd.rds
/usr/lib/R/site-library/ShortRead/Meta/vignette.rds
/usr/lib/R/site-library/ShortRead/NAMESPACE
/usr/lib/R/site-library/ShortRead/NEWS
/usr/lib/R/site-library/ShortRead/R/ShortRead
/usr/lib/R/site-library/ShortRead/R/ShortRead.rdb
/usr/lib/R/site-library/ShortRead/R/ShortRead.rdx
/usr/lib/R/site-library/ShortRead/script/qa-test.R
/usr/lib/R/site-library/ShortRead/template/0000-Header.html
/usr/lib/R/site-library/ShortRead/template/1000-Overview.html
/usr/lib/R/site-library/ShortRead/template/1100-Overview-SolexaRealign.html
/usr/lib/R/site-library/ShortRead/template/2000-RunSummary.html
/usr/lib/R/site-library/ShortRead/template/3000-ReadDistribution.html
/usr/lib/R/site-library/ShortRead/template/4000-CycleSpecific.html
/usr/lib/R/site-library/ShortRead/template/5000-PerTile.html
/usr/lib/R/site-library/ShortRead/template/6000-Alignment.html
/usr/lib/R/site-library/ShortRead/template/7000-MultipleAlignment.html
/usr/lib/R/site-library/ShortRead/template/8000-DepthOfCoverage.html
/usr/lib/R/site-library/ShortRead/template/9000-AdapterContamination.html
/usr/lib/R/site-library/ShortRead/template/9999-Footer.html
/usr/lib/R/site-library/ShortRead/template/image/bioclogo-small.gif
/usr/lib/R/site-library/ShortRead/template/QAAdapterContamination.html
/usr/lib/R/site-library/ShortRead/template/QA.css
/usr/lib/R/site-library/ShortRead/template/QAFiltered.html
/usr/lib/R/site-library/ShortRead/template/QAFlagged.html
/usr/lib/R/site-library/ShortRead/template/QAFooter.html
/usr/lib/R/site-library/ShortRead/template/QAFrequentSequence.html
/usr/lib/R/site-library/ShortRead/template/QAHeader.html
/usr/lib/R/site-library/ShortRead/template/QANucleotideByCycle.html
/usr/lib/R/site-library/ShortRead/template/QANucleotideUse.html
/usr/lib/R/site-library/ShortRead/template/QAQualityByCycle.html
/usr/lib/R/site-library/ShortRead/template/QAQualityUse.html
/usr/lib/R/site-library/ShortRead/template/QAReadQuality.html
/usr/lib/R/site-library/ShortRead/template/QASequenceUse.html
/usr/lib/R/site-library/ShortRead/template/qa_solexa.Rnw
/usr/lib/R/site-library/ShortRead/template/QASources.html
/usr/lib/R/site-library/ShortRead/unitTests/cases/PE_export.txt.gz
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_0001_int_head.txt.p
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_0001_nse_head.txt.p
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_0001_pos_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_results_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.9_lines.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_1_sequence.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_0001_realign_3col_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_0001_realign_head.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_export_run_as_factor.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/s_2_export_toIUPAC.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/sanger.fastq
/usr/lib/R/site-library/ShortRead/unitTests/cases/soap.txt
/usr/lib/R/site-library/ShortRead/unitTests/cases/solexa.fastq
/usr/lib/R/site-library/ShortRead/unitTests/test_AlignedRead.R
/usr/lib/R/site-library/ShortRead/unitTests/test_AllClasses.R
/usr/lib/R/site-library/ShortRead/unitTests/test_append.R
/usr/lib/R/site-library/ShortRead/unitTests/test_coverage.R
/usr/lib/R/site-library/ShortRead/unitTests/test_FastqFile.R
/usr/lib/R/site-library/ShortRead/unitTests/test_filterFastq.R
/usr/lib/R/site-library/ShortRead/unitTests/test_functions.R
/usr/lib/R/site-library/ShortRead/unitTests/test_Intensity.R
/usr/lib/R/site-library/ShortRead/unitTests/test_qa.R
/usr/lib/R/site-library/ShortRead/unitTests/test_readPrb.R
/usr/lib/R/site-library/ShortRead/unitTests/test_readQseq.R
/usr/lib/R/site-library/ShortRead/unitTests/test_readXStringColumns.R
/usr/lib/R/site-library/ShortRead/unitTests/test_renew.R
/usr/lib/R/site-library/ShortRead/unitTests/test_ShortReadQ.R
/usr/lib/R/site-library/ShortRead/unitTests/test_ShortRead.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SolexaIntensity.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRError.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRFilter.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRFilterResult.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRList.R
/usr/lib/R/site-library/ShortRead/unitTests/test_SRVector.R
/usr/lib/R/site-library/ShortRead/unitTests/test_trimEnds.R
/usr/lib/R/site-library/ShortRead/unitTests/test_trimTails.R
/usr/lib/R/site-library/ShortRead/unitTests/test_writeFastq.R
/usr/share/doc/r-bioc-shortread/changelog.Debian.gz
/usr/share/doc/r-bioc-shortread/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.

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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
1.64.0-3	trixie / main	amd64	Debian 13 · main · amd64	5.0 MiB	8.0 MiB	pool/main/r/r-bioc-shortread/r-bioc-shortread_1.64.0-3_amd64.deb
1.64.0-3	trixie / main	arm64	Debian 13 · main · arm64	5.0 MiB	8.1 MiB	pool/main/r/r-bioc-shortread/r-bioc-shortread_1.64.0-3_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.

1.64.0-3 / 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: ecb7f60bf6f2ab278508e9e1c96b07c07595b32e568323b876ab9c699434476a

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

printf '%s  %s\n' 'ecb7f60bf6f2ab278508e9e1c96b07c07595b32e568323b876ab9c699434476a' 'r-bioc-shortread_1.64.0-3_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

1.64.0-3 / 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: ba39393bcf2a2155ec8dff9f74fb55a6dae15e62242ba53c7ab348ac00830b47

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

printf '%s  %s\n' 'ba39393bcf2a2155ec8dff9f74fb55a6dae15e62242ba53c7ab348ac00830b47' 'r-bioc-shortread_1.64.0-3_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