Debian 12 (Bookworm) native package

r-bioc-shortread

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

Packages / Debian 12 (Bookworm) / gnu-r / r-bioc-shortread

Package: r-bioc-shortread (1.56.1-1)

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-base-core] (>= 4.2.2.20221110-1)
GNU R core of statistical computation and graphics system
dep: r-api-4.0
Package not available
dep: r-api-bioc-3.16
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-cran-hwriter]
HTML Writer - Outputs R objects in HTML format
dep: [r-bioc-zlibbioc]
(Virtual) zlibbioc Bioconductor package
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

Download r-bioc-shortread

Architecture	Package Size	Installed Size	Files
amd64	4.9 MiB	7.3 MiB	[list of files]
arm64	4.9 MiB	7.4 MiB	[list of files]

Percorsi file del pacchetto (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.pdf
/usr/lib/R/site-library/ShortRead/doc/Overview.R
/usr/lib/R/site-library/ShortRead/doc/Overview.Rnw
/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 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

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Versioni, suite e repository

Ogni riga è metadato dell'indice pacchetti per una versione, architettura, suite e repository. Nomi, URL e dimensioni arrivano dalla fonte; un link è un punto di recupero mutabile, non una redistribuzione OpenFactory.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
1.56.1-1	bookworm / main	amd64	Debian 12 · main · amd64	4.9 MiB	7.3 MiB	pool/main/r/r-bioc-shortread/r-bioc-shortread_1.56.1-1_amd64.deb
1.56.1-1	bookworm / main	arm64	Debian 12 · main · arm64	4.9 MiB	7.4 MiB	pool/main/r/r-bioc-shortread/r-bioc-shortread_1.56.1-1_arm64.deb

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Checksum e date di osservazione

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.

1.56.1-1 / 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: 77e4f7d4fbc234df0fcc60f6e389c1cbdb18fe03174603a85eb02955d6d58c9b

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

printf '%s  %s\n' '77e4f7d4fbc234df0fcc60f6e389c1cbdb18fe03174603a85eb02955d6d58c9b' 'r-bioc-shortread_1.56.1-1_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 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

1.56.1-1 / 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: af65a2dd22c59295520a47dfd606083d45253a6dcf550f5992559fe2007a44f0

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

printf '%s  %s\n' 'af65a2dd22c59295520a47dfd606083d45253a6dcf550f5992559fe2007a44f0' 'r-bioc-shortread_1.56.1-1_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 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Completezza del record

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 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Fonti e provenienza

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 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
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/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
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: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
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/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
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: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified