Evidence map›Paper›PMID 39763839›Full record

ArticlebioRxiv : the preprint server for biology2024

sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing.

Roozbeh Dehghannasiri, Marek Kokot, Alexander L Starr, Jamie Maziarz, Tal Gordon, Serena Y Tan, Peter L Wang, Ayelet Voskoboynik, Jacob M Musser, Sebastian Deorowicz and 1 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Roozbeh DehghannasiriDepartment of Biomedical Data Science, Stanford University, Stanford, 94305, USA.ORCID 0000-0001-7413-3437
Marek KokotDepartment of Algorithmics and Software, v, Gliwice, Poland.ORCID 0000-0002-6420-1587
Alexander L StarrDepartment of Biology, Stanford University, Stanford, 94305, USA.
Jamie MaziarzDepartment of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, 06511, USA.
Tal GordonInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, 94305 USA.
Serena Y TanDepartment of Pathology, Stanford University Medical Center, Stanford, 94305, USA.
Peter L WangDepartment of Biomedical Data Science, Stanford University, Stanford, 94305, USA.
Ayelet VoskoboynikDepartment of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, 93950, USA.ORCID 0000-0001-9570-1392
Jacob M MusserDepartment of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, 06511, USA.ORCID 0000-0002-6163-5152
Sebastian DeorowiczDepartment of Algorithmics and Software, v, Gliwice, Poland.ORCID 0000-0002-9496-733X
Julia SalzmanDepartment of Biomedical Data Science, Stanford University, Stanford, 94305, USA.ORCID 0000-0001-7630-3436

Funding

Computational- and experimental- driven discovery of splicing regulation and circRNA functionR35GM139517 · NIGMS · STANFORD UNIVERSITY · PI Julia Salzman · 2021 to 2026
$2.9M
Evolutionary Conserved Mechanisms that Control Central Nervous System Development Regeneration and DegenerationR01AG076908 · NIA · STANFORD UNIVERSITY · PI Ayelet Voskoboynik · 2022 to 2026
$1.9M
High Performance Computing Instrumentation for the Yale Center for Genome AnalysisS10OD030363 · OD · YALE UNIVERSITY · PI MANE, SHRIKANT M · 2022 to 2022
$1.2M
NIA NIH HHS R01 AG076908NIGMS NIH HHS R35 GM139517NIH HHS S10 OD030363
6 · The paper itself

Abstract

Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J recombination, and is blind to sequences missing from imperfect reference genomes. Here, we present sc-SPLASH, a highly efficient pipeline that extends our SPLASH framework for statistics-first, reference-free discovery to barcoded scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium); we also provide its optimized module for preprocessing and

Identifiers

PMID39763839
PMCPMC11703226

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.