Canonical record
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
pmid:27508061
Imported paper
A paper the journal holds from the corpus, with its canonical record and every version of it. The journal has not analysed it.
Versions held 2 Every version of this record the journal holds. A version is identified by its content hash and does not change, so a version a reader downloaded yesterday is still the version they downloaded.
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Revision 4 offered by the Corpus Engine
sha256:55ea50e300bb431a86d436951ca0ffa6f4e183dc3cde24b554526da6a21d4402
.sci 1.5 · held 2026-11-08T18:43:31+00:00
- assay:1 rna-seq-read-alignment 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:2 rna-seq-gene-quantification 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:3 rna-seq-count-filtering-and-normalisation 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:4 rna-seq-differential-expression 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:5 rna-seq-pathway-enrichment 0.1.0 This entry names no record, so the journal cannot say what it was run against.
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Revision 7 offered by the Corpus Engine
sha256:72abc1c558c8d6a3461ec0365234046ee2dc5f723b2f8b3b3ae0904ac6e4ab85
.sci 1.5 · held 2026-11-08T19:04:22+00:00
- assay:1 rna-seq-read-alignment 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:2 rna-seq-gene-quantification 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:3 rna-seq-count-filtering-and-normalisation 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:4 rna-seq-differential-expression 0.1.0 This entry names no record, so the journal cannot say what it was run against.
- assay:5 rna-seq-pathway-enrichment 0.1.0 This entry names no record, so the journal cannot say what it was run against.
Reviewer decisions A decision names the exact version it was made against — its revision, its content hash and the hash of the bytes that were read — and the runs it rests on. A decision that does not name a version is not published, because a reader would not be able to say what was in front of the reviewer.
No reviewer decision is recorded against this record. Until one is, the record is held as it is: an imported paper, an analysis result, or an open fork.
The samples analysed The cohort the paper states, beside the count the repository holds of the data it published. Where the two differ, a run over the repository's samples analysed a different cohort from the one the paper analysed.
The paper states a cohort of 12 samples, and the repository's own count of the data it holds is also 12 samples. The counts agree. The journal has not checked that they are the same samples, and does not say they are.
The cohort the paper states
12 samples
- B.virgin
- 2
- L.virgin
- 2
- B.pregnant
- 2
- L.pregnant
- 2
- B.lactating
- 2
- L.lactating
- 2
There are therefore six groups of RNA samples, one for each combination of cell type and mouse status. Two biological replicates were collected for each group.
The repository's own count
12 samples
- Basal 2 dL
- 2
- Basal virgin
- 2
- Luminal 2 dL
- 2
- Basal 18.5 dP
- 2
- Luminal virgin
- 2
- Luminal 18.5 dP
- 2
The sample titles of the GEO series: Basal 18.5 dP (2), Basal 2 dL (2), Basal virgin (2), Luminal 18.5 dP (2), Luminal 2 dL (2), Luminal virgin (2).
Stated by revision 7 of pmid:27508061, published by corpus_engine as .sci 1.5.
The assays in this record, and what ran against them 5 The assays the head of this record carries, and the result each one was answered with. The journal did not compute any of it: the provider ran the assay, and the journal holds the result as it was returned, with the hashes that identify it. The numbers below are the provider's own.
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assay:1 0.1.0
rna_seq_read_alignment
This entry names no record, so the journal cannot say what it was run against.
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assay:2 0.1.0
gene_count_quantification
Uses output from assay:1
This entry names no record, so the journal cannot say what it was run against.
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assay:3 0.1.0
normalise_counts, normalise_counts_tmm
Uses output from assay:2
This entry names no record, so the journal cannot say what it was run against.
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assay:4 0.1.0
differential_expression_fit, fdr_bh, differential_expression_quasi_likelihood
Uses output from assay:3
This entry names no record, so the journal cannot say what it was run against.
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assay:5 0.1.0
pathway_enrich
Uses output from assay:4
This entry names no record, so the journal cannot say what it was run against.
The runs the journal holds for this record 7 The provider ran these and the journal holds what was returned, with the hashes that identify it. The journal ran none of them and recomputed none of them.
The journal holds no completed run of this analysis for this record.
The journal holds no completed run of this analysis for this record.
The answer the journal stands behind is the run of rna_seq_differential_expression 0.1.0 that named no version of this record the journal holds. It analysed an unstated number of samples. The journal holds 2 results for this analysis and publishes each of them, with the reason it is not the answer.
The answer the journal stands behind is the run of rna_seq_pathway_enrichment 0.1.0 that named no version of this record the journal holds. It analysed an unstated number of samples.
The answer the journal stands behind is the run of rna_seq_count_filtering_and_normalisation 0.1.0 that named no version of this record the journal holds. It analysed an unstated number of samples. The journal holds 2 results for this analysis and publishes each of them, with the reason it is not the answer.
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rna_seq_read_alignment 0.1.0 refused
This run did not finish, so it is not an answer to anything.
7daff85e-0e95-4e29-b922-1bf66aa96252
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:be55ead2068cf19cc9efd01d113aa3057e4b3dde2343ea0ecd4562aaf2d1bd0e
- Evidence hash
- 48eb942441653112489a7ce4ff0821a719728c1188aeab486161fb93c17ec872
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
-
rna_seq_gene_quantification 0.1.0 refused
This run did not finish, so it is not an answer to anything.
8573fa99-85cd-4f56-bdd5-3651d1cdfd58
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:43cac33f2a7f97f767d87937964e805d3ae6fab5b695818b5cf7d37efdb790fb
- Evidence hash
- 0e116046745cbd0ed15ae537d918f4776dfa6563908c644dbdf2221600f760ed
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
-
rna_seq_differential_expression 0.1.0 complete
The journal recorded this run before the one it stands behind, and still holds it.
85f9fdf4-4c2e-4155-8daa-da11d28021ef
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:0da96b2fe1f4ab61ad9ec91f1a9130268fb314dd354d6b6f623388f5e7ae9d4c
- Evidence hash
- 899e82b58fd83ec21bfd48461d0797f7867bbd5dedf5744ed19b8654b456e291
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
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rna_seq_pathway_enrichment 0.1.0 complete · the answer
This is the answer the journal stands behind. The run named no version of this record that the journal holds, so it is the answer on the ground that it is the last run the journal recorded.
91daa9a9-2b77-45e0-8727-13a7643efe9d
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:6daad652773fe321cd885609fcc97c1378b769fa9173daaf172c33582fb30efb
- Evidence hash
- d1d756c2c34777bc09aa0d236928ddd951666073cec97e52acd028342d3ed85f
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
-
rna_seq_differential_expression 0.1.0 complete · the answer
This is the answer the journal stands behind. The run named no version of this record that the journal holds, so it is the answer on the ground that it is the last run the journal recorded.
a92cdcdd-e95c-4579-a4dd-7648d2c24eff
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:194ba83e9468a04462de791795cd0bdf4bbdc992bb5cea0b420fa659fe8ecc1f
- Evidence hash
- ffd49280b7bcfa17e938f077569600a4d38d3dce873176d5f4f8f5aa230659da
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
-
rna_seq_count_filtering_and_normalisation 0.1.0 complete
The journal recorded this run before the one it stands behind, and still holds it.
cb681050-44e5-43c9-801c-87e82a09ed55
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:b681c5238c00d87068957502cabb988094a393818da50840119649867a1fb4df
- Evidence hash
- f7288a5fdb3282fea31889580c03db42473612241a6fed77527aa211540c6df3
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
-
rna_seq_count_filtering_and_normalisation 0.1.0 complete · the answer
This is the answer the journal stands behind. The run named no version of this record that the journal holds, so it is the answer on the ground that it is the last run the journal recorded.
fa44f761-7022-4c3f-975f-d8ce85abd2a8
- Samples analysed
- not stated
- Run against
- the run named no version
- Result hash stated by the provider
- sha256:a1f4df7f4ba128a759d8da6db62614641875603a7474e4c02572b23b18563976
- Evidence hash
- 25d0e73c4e732aef23de129367c22fb8c3889275e672ff9c8be9c63fdd553a59
This run states no sample count, so the cohort it used cannot be set against the cohort the paper states.
Forks opened from this record A fork is somebody's work on a version of this record, held by the journal under its own identifier so that the master stays the master. Each one is an open merge request against this record, and each says what it changed.
Nothing has been forked from this record. A fork arrives when a platform opens a version, works on it and offers it back to the journal under its own identifier.