ArticleBioinformatics (Oxford, England)2023
scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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.
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.
Who cites it
74 citing papers in PubMed.
- Using In Silico Pseudobulk Differential Expression and Trajectory Analysis of Single Cell RNA Sequencing to Reveal Stem Cell State Transitions in Colonic Inflammation.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Article
- Atlas of cell types and regulatory elements underlying human facial diversity.Nature genetics · 2026Article
- Spatially resolved multiomics of human meningeal development reveal lineage and disease dynamics.Nature cell biology · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
- Article
- The DLX/Notch axis is necessary for spatiotemporal regulation of neural cell fate.Nature communications · 2026Article
- Article
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- Single cell multiomics unravel the transcription networks controlling the different EMT tumor states.Nature communications · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- Tissue-resident neutrophils serve homeostatic and immunological functions in embryos.Nature communications · 2026Article
- Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem.Science advances · 2026Article
- Mapping the transcriptional diversity of calcium signaling in the mouse and human brain.iScience · 2026Article
- Single-cell and spatial transcriptomic analyses of gene therapy-associated retinal inflammation in non-human primates.Molecular therapy. Advances · 2026Article
- Role of SCAP in regulation of pancreatic homeostasis, pancreatitis, and tumorigenesis.Oncogene · 2026Article
- Intrinsic regulation of intestinal stem cell fate and homeostasis by Tet.bioRxiv : the preprint server for biology · 2026Article
- Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Blocking apoptosis promotes survival and alters developmental dynamics of human retinal ganglion cells in retinal organoids.Cell reports · 2026Article
- Developmental determinants of male bias in medulloblastoma.bioRxiv : the preprint server for biology · 2026Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
summaryscFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a focus on cell biasing and fate splits at the level of bifurcations. It is meant to be fully integrated into the scanpy ecosystem for seamless analysis of trajectories from single-cell data of various modalities (e.g. RNA and ATAC). AVAILABILITY AND IMPLEMENTATION: scFates is released as open-source software under the BSD 3-Clause 'New' License and is available from the Python Package Index at https://pypi.org/project/scFates/. The source code is available on GitHub at https://github.com/LouisFaure/scFates/. Code reproduction and tutorials on published datasets are available on GitHub at https://github.com/LouisFaure/scFates_notebooks. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.