On the public citation graph

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

https://doi.org/10.1093/gigascience/giaa102

0 signed · 68 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2008.09.050openalex-snapshot

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

inferredcites →https://doi.org/10.1016/j.cels.2018.03.014openalex-snapshot

Practical Computational Reproducibility in the Life Sciences

inferredcites →https://doi.org/10.1016/j.cels.2018.05.012openalex-snapshot

Community-Driven Data Analysis Training for Biology

inferredcites →https://doi.org/10.1016/j.coisb.2017.12.007openalex-snapshot

Methods and challenges in the analysis of single-cell RNA-sequencing data

inferredcites →https://doi.org/10.1016/j.gpb.2020.02.005openalex-snapshot

Direct Comparative Analyses of 10X Genomics Chromium and Smart-Seq2

inferredcites →https://doi.org/10.1038/550451aopenalex-snapshot

The Human Cell Atlas: from vision to reality

inferredcites →https://doi.org/10.1038/nature14966openalex-snapshot

Single-cell messenger RNA sequencing reveals rare intestinal cell types

inferredcites →https://doi.org/10.1038/nbt.3192openalex-snapshot

Spatial reconstruction of single-cell gene expression data

inferredcites →https://doi.org/10.1038/nbt.3711openalex-snapshot

Revealing the vectors of cellular identity with single-cell genomics

inferredcites →https://doi.org/10.1038/ncomms13182openalex-snapshot

Massive and parallel expression profiling using microarrayed single-cell sequencing

inferredcites →https://doi.org/10.1038/ncomms14049openalex-snapshot

Massively parallel digital transcriptional profiling of single cells

inferredcites →https://doi.org/10.1038/nmeth.3174openalex-snapshot

bam.iobio: a web-based, real-time, sequence alignment file inspector

inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot

Salmon provides fast and bias-aware quantification of transcript expression

inferredcites →https://doi.org/10.1038/nmeth.4644openalex-snapshot

scmap: projection of single-cell RNA-seq data across data sets

inferredcites →https://doi.org/10.1038/nmeth.4662openalex-snapshot

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

inferredcites →https://doi.org/10.1038/s41467-016-0009-6openalex-snapshot

In situ click chemistry generation of cyclooxygenase-2 inhibitors

inferredcites →https://doi.org/10.1038/s41586-019-0969-xopenalex-snapshot

The single-cell transcriptional landscape of mammalian organogenesis

inferredcites →https://doi.org/10.1038/s41592-018-0046-7openalex-snapshot

Bioconda: sustainable and comprehensive software distribution for the life sciences

inferredcites →https://doi.org/10.1038/s41592-019-0535-3openalex-snapshot

Supervised classification enables rapid annotation of cell atlases

inferredcites →https://doi.org/10.1038/s41592-019-0654-xopenalex-snapshot

Orchestrating single-cell analysis with Bioconductor

inferredcites →https://doi.org/10.1038/s41592-021-01102-wopenalex-snapshot

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

inferredcites →https://doi.org/10.1088/1742-5468/2008/10/p10008openalex-snapshot

Fast unfolding of communities in large networks

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btw777openalex-snapshot

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

inferredcites →https://doi.org/10.1093/bioinformatics/bty711openalex-snapshot

WIlsON: Web-based Interactive Omics VisualizatioN

inferredcites →https://doi.org/10.1093/gigascience/giz144openalex-snapshot

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses

inferredcites →https://doi.org/10.1093/nar/gky379openalex-snapshot

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

inferredcites →https://doi.org/10.1101/009944openalex-snapshot

Phinch: An interactive, exploratory data visualization framework for –Omic datasets

inferredcites →https://doi.org/10.1101/gr.209601.116openalex-snapshot

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

inferredcites →https://doi.org/10.1111/2041-210x.12945openalex-snapshot

Wallace : A flexible platform for reproducible modeling of species niches and distributions built for community expansion

inferredcites →https://doi.org/10.1126/science.aar5780openalex-snapshot

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

inferredcites →https://doi.org/10.1186/s13059-016-0938-8openalex-snapshot

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq

inferredcites →https://doi.org/10.1186/s13059-016-0947-7openalex-snapshot

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

inferredcites →https://doi.org/10.1186/s13059-017-1381-1openalex-snapshot

RNA virus interference via CRISPR/Cas13a system in plants

inferredcites →https://doi.org/10.1186/s13059-017-1382-0openalex-snapshot

SCANPY: large-scale single-cell gene expression data analysis

inferredcites →https://doi.org/10.1186/s13059-018-1486-1openalex-snapshot

HiGlass: web-based visual exploration and analysis of genome interaction maps

inferredcites →https://doi.org/10.1186/s13059-019-1663-xopenalex-snapshot

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

inferredcites →https://doi.org/10.1186/s13059-019-1670-yopenalex-snapshot

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

inferredcites →https://doi.org/10.1186/s13059-019-1862-5openalex-snapshot

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data

inferredcites →https://doi.org/10.1371/journal.pcbi.1006361openalex-snapshot

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

inferredcites →https://doi.org/10.15252/msb.20188746openalex-snapshot

Current best practices in single‐cell RNA‐seq analysis: a tutorial

inferredcites →https://doi.org/10.18129/b9.bioc.singlecellexperimentopenalex-snapshot

SingleCellExperiment

inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot

UMAP: Uniform Manifold Approximation and Projection

inferredcites →https://doi.org/10.3233/978-1-61499-649-1-87openalex-snapshot

Jupyter Notebooks – a publishing format for reproducible computational workflows

inferredcites →https://doi.org/10.48550/arxiv.1802.03426openalex-snapshot

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

inferredcites →https://doi.org/10.5167/uzh-162597openalex-snapshot

The Human Cell Atlas

inferredcites →https://doi.org/10.5281/zenodo.3235020openalex-snapshot

chanzuckerberg/cellxgene: Release 0.10.0

inferredcites →https://doi.org/10.6084/m9.figshare.951915openalex-snapshot

Phinch: An interactive, exploratory data visualization framework for metagenomic datasets

inferredcites →https://doi.org/10.7554/elife.27041openalex-snapshot

The Human Cell Atlas

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4132724openalex-extracted

Delayed Booster Dosing Improves Human Antigen-Specific IG and B Cell Responses to the RH5.1/AS01 B Malaria Vaccine

inferred← citeshttps://doi.org/10.1002/cpz1.31openalex-snapshot

Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update

inferred← citeshttps://doi.org/10.1016/bs.apcsb.2022.11.015openalex-snapshot

A compilation of bioinformatic approaches to identify novel downstream targets for the detection and prophylaxis of cancer

inferred← citeshttps://doi.org/10.1016/j.ccell.2021.07.004openalex-snapshot

From bench to bedside: Single-cell analysis for cancer immunotherapy

inferred← citeshttps://doi.org/10.1016/j.xgen.2025.101005openalex-snapshot

Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025

inferred← citeshttps://doi.org/10.1038/s41592-021-01102-wopenalex-snapshot

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

inferred← citeshttps://doi.org/10.1080/14789450.2023.2265062openalex-snapshot

A Galaxy of informatics resources for MS-based proteomics

inferred← citeshttps://doi.org/10.1093/gigascience/giad091openalex-snapshot

Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis

inferred← citeshttps://doi.org/10.1093/nargab/lqae134openalex-snapshot

scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison

inferred← citeshttps://doi.org/10.1093/plphys/kiac468openalex-snapshot

Toward a data infrastructure for the Plant Cell Atlas

inferred← citeshttps://doi.org/10.1101/2020.04.15.043737openalex-snapshot

UNCURL-App: Interactive database-driven analysis of scRNA-Seq data

inferred← citeshttps://doi.org/10.1101/2021.08.16.456499openalex-snapshot

scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data

inferred← citeshttps://doi.org/10.1101/2022.11.24.517172openalex-snapshot

Inhibition of myeloperoxidase attenuates thoracic aortic aneurysm formation in Marfan disease

inferred← citeshttps://doi.org/10.1145/3638243openalex-snapshot

Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice

inferred← citeshttps://doi.org/10.1146/annurev-animal-111523-102217openalex-snapshot

Comparative Genomics and Epigenomics of Transcriptional Regulation

inferred← citeshttps://doi.org/10.1172/jci.insight.163859openalex-snapshot

Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010752openalex-snapshot

Galaxy Training: A powerful framework for teaching!

inferred← citeshttps://doi.org/10.3389/fgene.2024.1460351openalex-snapshot

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

inferred← citeshttps://doi.org/10.64898/2026.06.11.731578openalex-snapshot

oxo-flow: compiled, memory-safe bioinformatics workflow orchestration

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.