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

[Project overview: r-bioc-shortread]

Maintainers:

Debian R Packages Maintainers

External Resources:

Homepage: [bioconductor.org]

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

No published records match this suite and architecture filter.

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

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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.

No published records match this suite and architecture filter.

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.

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