sci_record · open
Corpus Engine
pmid:27508061version sci 1.5 revision 7 · sha256 sha256:72abc1c558c8d6a3461ec0365234046ee2dc5f723b2f8b3b3ae0904ac6e4ab85
Home
/
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
submitted
Original research
revision 0
1 days open
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Evidence at a glance
No scientific verdict has been recorded. Explore the available material or start a research fork.
- Registered claims
- 0
- Journal analysis runs
- 0
- Research forks opened
- 2
Paper record The research question, publication details and source material recorded for this paper.
In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.
Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
- Intake
- Imported as a canonical record
- Recorded by
- Journal Editor
- Ingest source
- F1000Research · pmid:27508061
- DOI
- 10.12688/f1000research.8987.2
- Source text held
- The abstract only
Data sources Sources named by the paper, including data, code and protocols. Check the recorded access and verification status before preparing a run.
source_text · open
Source text
https://doi.org/10.12688/f1000research.8987.2· sha256 sha256:3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb
source_text · open
Source text
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE60450&format=file&file=GSE60450_Lactation-GenewiseCounts.txt.gz· sha256 sha256:906b6ec4c33e95ca0ba454a3e0d07ad74e9cb7528ee38b89a9b122f5674a5f0d
source_text · open
Source text
https://bioconductor.org/packages/3.3/data/annotation/src/contrib/org.Mm.eg.db_3.3.0.tar.gzversion 3.3.0 · sha256 sha256:5dc93707b7ca319b295b5b19963c573d5a3817d836f458a3e30d635ddd4e2365
source_text · open
Source text
http://bioinf.wehi.edu.au/edgeR/F1000Research2016/targets.txt· sha256 sha256:88ae42c0539403073f0bbbd53287dd9c9cf61ddd5b1a42856243d7d99113cb8b
source_text · open
Source text
http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.R· sha256 sha256:3b11478ac314c4456af8b4ba7af7992e938488ffc7bec88d3f73f42aed4c0bba
source_text · open
Source text
http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.Rnw· sha256 sha256:defd3acb73dcbfe885ca02209ac9437b785b4ccf12c7ba09a8a8bb311173902d
source_text · open
Source text
http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.pdf· sha256 sha256:76ea4da65b151b1bb78ba42b0d80c0e864632df0e13219fe968525a43efd2276
Papers built from this record Other journal records made from this one — an analysis of its published figures, or a fork of it. They are separate records, with their own verdicts and their own limits.
Peer review forks Follow attempts to repeat or extend this paper. Each fork records its question, progress and results.
replication · version 1
The paper's own analysis finds more than 5000 differentially expressed genes at a false discovery rate of 5% between the basal pregnant and lactating groups, and its printout shows the top gene Csn1s2b with a log2 fold change of 6.08.
not established
replication · version 1
Between basal lactating and basal pregnant mice, the edgeR quasi-likelihood F-test calls 5245 differentially expressed genes at a false discovery rate of 5%, and the top gene is Csn1s2b with a log2 fold change of 6.08.
not established
Start a research fork to check a result or build on this work. Choose the result you want to reproduce after signing in.
Sign in to start a forkThe readings the journal made no reading yet Readings the journal made itself, from the text it holds, by two providers asked the same questions. They are readings, not replications: nothing has been run.
The readers did not agree
Two readings of the same source text, and whether they agreed on the decisive fields.
The readers did not agree
Two readings of the same source text, and whether they agreed on the decisive fields.
The result no result yet The recorded finding, its explanation and the publication decision.
Scientific verdict — what the evidence supports
No scientific verdict
Nothing has been adjudicated on the evidence yet. An editorial decision may still close this record, and that is not a result.
Editorial disposition — what the desk does with it
No disposition
The desk has recorded no decision on this submission.
Assessments and commentary 0 critiques Read model-generated assessments and attributed researcher discussion alongside the recorded results.
Automated assessments
Opinion — non-bindingNo automated assessment is available.
no language-model credential is configured, so no machine critique can be produced
No verified model response is available for publication.
Researcher commentary
Opinion — non-bindingNo researcher commentary has been recorded yet.
Scope and unresolved questions Review the scope of the analysis, any missing runs and claims that still need evidence.
Out of scope by construction (0)
- No verdict has been computed, so no scope statement exists yet.
Registered runs that never answered (0)
- Every registered order produced an accepted attempt.
Registered cells with no evidence (0)
- Every registered cell carries at least one observation.
Claim map 0 claims What was registered before anything ran: the number to land on, the band it has to land in, and how many runs were promised. The bands were frozen before any output existed, and whether a result falls inside a band is the engine's answer.
This submission carries no registered claim, so no comparison plan exists. The engine refuses to compute a verdict without one.
Registered execution runs 0 runs Every order that was on record before dispatch, and what each one produced. A missing attempt is a discrepancy, not a quiet omission.
| Order | Condition | State | Attempts | Accepted | Observations |
|---|---|---|---|---|---|
| No execution order has been registered for this submission. | |||||
Analyses run by a provider 7 runs Analyses that another application ran against the exact version of this record, and what they found. The journal holds the run and its provenance; it did not run the analysis itself, and an analysis is not a replication of the paper's experiment.
| Analysis | Provider | State | What it found | Record version it ran against |
|---|---|---|---|---|
| Read alignment rna_seq_read_alignment 0.1.0 7daff85e-0e95-4e29-b922-1bf66aa96252 | automated assays | refused | refused | No version was named, so the run is held unbound. The targets file the workflow reads has a row with 5 fields and a header with 4, so the samples the workflow runs cannot be read. The record gives that assay the name 'assay:1'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
| Gene quantification rna_seq_gene_quantification 0.1.0 8573fa99-85cd-4f56-bdd5-3651d1cdfd58 | automated assays | refused | refused | No version was named, so the run is held unbound. The quantification assay counts the reads of the alignment assay, and no alignment file was given to it. The alignments are named in the request, and each one is bound to the execution that produced it. The record gives that assay the name 'assay:2'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
| Differential expression (edgeR quasi-likelihood) rna_seq_differential_expression 0.1.0 85f9fdf4-4c2e-4155-8daa-da11d28021ef | automated assays | complete | complete | No version was named, so the run is held unbound. The assay ran the published method and its outputs were recorded. Whether those outputs agree with the paper's published values is a separate analysis of the saved outputs, and it is not part of this run. The record gives that assay the name 'assay:4'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
| Pathway analysis (GO, KEGG, fry, camera) rna_seq_pathway_enrichment 0.1.0 91daa9a9-2b77-45e0-8727-13a7643efe9d | automated assays | complete | complete | No version was named, so the run is held unbound. The assay reproduces the paper's published values. The record gives that assay the name 'assay:5'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
| Differential expression (edgeR quasi-likelihood) rna_seq_differential_expression 0.1.0 a92cdcdd-e95c-4579-a4dd-7648d2c24eff | automated assays | complete | complete | No version was named, so the run is held unbound. The assay reproduces the paper's published values. The record gives that assay the name 'assay:4'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
| Count filtering, normalisation and sample quality rna_seq_count_filtering_and_normalisation 0.1.0 cb681050-44e5-43c9-801c-87e82a09ed55 | automated assays | complete | complete | No version was named, so the run is held unbound. The assay ran the published method and its outputs were recorded. Whether those outputs agree with the paper's published values is a separate analysis of the saved outputs, and it is not part of this run. The record gives that assay the name 'assay:3'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
| Count filtering, normalisation and sample quality rna_seq_count_filtering_and_normalisation 0.1.0 fa44f761-7022-4c3f-975f-d8ce85abd2a8 | automated assays | complete | complete | No version was named, so the run is held unbound. The assay reproduces the paper's published values. The record gives that assay the name 'assay:3'. The run names no version of the record in its sealed manifest, so it is held unbound. No source version has been inferred for it. |
Ledger events for this receipt 30 events The append-only log behind this record. Each event is hashed and signed and links to the one before it, so the history can be checked rather than trusted.
| Seq | Event | Actor | Recorded | Event hash |
|---|---|---|---|---|
| 5373 | submission.received | admin+journal-prd@bntrg.co.uk intake_service | 2026-11-08T18:58:45.016247Z | b86abc48fd9e144ea241af3e… |
| 5374 | paper.sci_version_held | corpus_engine external_service | 2026-11-08T18:58:45.040436Z | a502f529be904e265a3c991c… |
| 5375 | peer_review.replication_started | admin+journal-prd@bntrg.co.uk fork_operator | 2026-11-08T19:04:11.651535Z | bd761e7316eb63ad483173b5… |
| 5376 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:11.665117Z | 07175f0f655d4b157c3e2180… |
| 5377 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:11.671136Z | 5e66614cbc3a6b9336c95a2b… |
| 5378 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:11.677130Z | 695532ca7e4ceb60d46a903b… |
| 5379 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:11.682441Z | a10b3f1cd61984451c1ae5fd… |
| 5380 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:11.699346Z | 7e1df55573b3d4579e5939e0… |
| 5381 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:11.709313Z | 8324c47124b948a8040c4f96… |
| 5382 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:11.735561Z | 18b9ba057c22523434dec3f8… |
| 5383 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:11.783150Z | b3e93171b294974b602067ab… |
| 5384 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:11.903502Z | 47477250a6155ea2069eea8b… |
| 5385 | paper.execution_evidence_recorded | admin+journal-prd@bntrg.co.uk evidence_intake_service | 2026-11-08T19:04:12.038594Z | a7c8ce0ddf981d96bb46258a… |
| 5428 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:12.821449Z | 9062473816d58baa6505d623… |
| 5429 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:12.969003Z | e9dd7f7a26b301346fa34a02… |
| 5430 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:12.988121Z | 94441c0e8e974a9f0ada722e… |
| 5431 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:13.014985Z | d1c91778e5cc2c54d70dd079… |
| 5432 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:13.043414Z | c8a6701f1f4b1b5aa9dbe3fc… |
| 5433 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-08T19:04:13.056156Z | 9647cf4c25e0be7df56e59ba… |
| 5452 | paper.sci_version_held | corpus_engine external_service | 2026-11-08T19:04:27.165188Z | 45fdc71c02546f8b93892875… |
| 5453 | peer_review.replication_started | admin+journal-prd@bntrg.co.uk fork_operator | 2026-11-09T00:48:18.425348Z | b842843e0e772bad395a3a6b… |
| 5454 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:18.472160Z | 16fa2d7599af442d299b1583… |
| 5455 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:18.507481Z | 875da5066989d618774dfa0a… |
| 5456 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:18.526355Z | 3ab0178be638d92ba7875e5d… |
| 5499 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:20.485407Z | 3a0d3dcd1b8f80bd1784e5b3… |
| 5500 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:20.605780Z | ea43cbd86ea338a9adfe6c37… |
| 5501 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:20.630371Z | c48b5c2ea716e7752a05b4a9… |
| 5502 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:20.647690Z | 61ecae7ba271fd61cc6aed4d… |
| 5503 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:20.682113Z | 357a4b4fb4804cc5e90c0db3… |
| 5504 | peer_review.stage_recorded | peer-review-engine automated_assessor | 2026-11-09T00:48:20.705401Z | 772fd0a64a5da5ee24604406… |
Downloads and public API Machine-readable records for developers, reuse and independent verification.
- Record ID
- 7bab332b-5c5b-40ab-a2c6-ce7da66e3417
- Package hash
- 509bdc13bb77e0d3d0d3df7c3de51f5b6ec998ea74675aa7d20236577adbeb36