{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2013:QVSQHWCOBDD5FNGR6MPUO5HGGN","short_pith_number":"pith:QVSQHWCO","schema_version":"1.0","canonical_sha256":"856503d84e08c7d2b4d1f31f4774e6335154cb7f32826415883f8e530075a607","source":{"kind":"arxiv","id":"1308.3172","version":1},"attestation_state":"computed","paper":{"title":"Realistic simulations reveal extensive sample-specificity of RNA-seq biases","license":"http://creativecommons.org/licenses/by-nc-sa/3.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Botond Sipos, Greg Slodkowicz, Nick Goldman, Tim Massingham","submitted_at":"2013-08-14T16:26:29Z","abstract_excerpt":"In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of competing correction methods. We introduce the first framework to reproduce the properties of individual RNA-seq runs and, by applying it on several datasets, we demonstrate the importance of accounting for sample-specificity in realistic simulations."},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1308.3172","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/3.0/","primary_cat":"q-bio.GN","submitted_at":"2013-08-14T16:26:29Z","cross_cats_sorted":[],"title_canon_sha256":"268184bd9ed700d1c36381ea710b29c0b2c94d1438306ddfd1515bc769ef6ed9","abstract_canon_sha256":"c353d424c81b3f78818a425bd0f31fdb71525e1e26ed1ac9ffd7013966a3e88b"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:15:56.442049Z","signature_b64":"3p2ilbgenmLxJ1UFqPyEaIoQFw5A1jMinZSDOrl2gtQoUNzYxtq42gA8d24q+K7ZuShCg75++EFy0Sggjgx/BA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"856503d84e08c7d2b4d1f31f4774e6335154cb7f32826415883f8e530075a607","last_reissued_at":"2026-05-18T03:15:56.441343Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:15:56.441343Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Realistic simulations reveal extensive sample-specificity of RNA-seq biases","license":"http://creativecommons.org/licenses/by-nc-sa/3.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Botond Sipos, Greg Slodkowicz, Nick Goldman, Tim Massingham","submitted_at":"2013-08-14T16:26:29Z","abstract_excerpt":"In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of competing correction methods. We introduce the first framework to reproduce the properties of individual RNA-seq runs and, by applying it on several datasets, we demonstrate the importance of accounting for sample-specificity in realistic simulations."},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1308.3172","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"aliases":[{"alias_kind":"arxiv","alias_value":"1308.3172","created_at":"2026-05-18T03:15:56.441461+00:00"},{"alias_kind":"arxiv_version","alias_value":"1308.3172v1","created_at":"2026-05-18T03:15:56.441461+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1308.3172","created_at":"2026-05-18T03:15:56.441461+00:00"},{"alias_kind":"pith_short_12","alias_value":"QVSQHWCOBDD5","created_at":"2026-05-18T12:27:57.521954+00:00"},{"alias_kind":"pith_short_16","alias_value":"QVSQHWCOBDD5FNGR","created_at":"2026-05-18T12:27:57.521954+00:00"},{"alias_kind":"pith_short_8","alias_value":"QVSQHWCO","created_at":"2026-05-18T12:27:57.521954+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN","json":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN.json","graph_json":"https://pith.science/api/pith-number/QVSQHWCOBDD5FNGR6MPUO5HGGN/graph.json","events_json":"https://pith.science/api/pith-number/QVSQHWCOBDD5FNGR6MPUO5HGGN/events.json","paper":"https://pith.science/paper/QVSQHWCO"},"agent_actions":{"view_html":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN","download_json":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN.json","view_paper":"https://pith.science/paper/QVSQHWCO","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1308.3172&json=true","fetch_graph":"https://pith.science/api/pith-number/QVSQHWCOBDD5FNGR6MPUO5HGGN/graph.json","fetch_events":"https://pith.science/api/pith-number/QVSQHWCOBDD5FNGR6MPUO5HGGN/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN/action/timestamp_anchor","attest_storage":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN/action/storage_attestation","attest_author":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN/action/author_attestation","sign_citation":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN/action/citation_signature","submit_replication":"https://pith.science/pith/QVSQHWCOBDD5FNGR6MPUO5HGGN/action/replication_record"}},"created_at":"2026-05-18T03:15:56.441461+00:00","updated_at":"2026-05-18T03:15:56.441461+00:00"}