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genesorteR: Feature Ranking in Clustered Single Cell Data

https://doi.org/10.1101/676379
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What this work says

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

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Comprehensive Integration of Single-Cell Data
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Valid Post-Clustering Differential Analysis for Single-Cell RNA-Seq
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Finding significant keywords for document databases by two-phase Maximum Entropy Partitioning
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A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot
Integrative genomics viewer
inferredcites →https://doi.org/10.1038/ncomms14049openalex-snapshot
Massively parallel digital transcriptional profiling of single cells
inferredcites →https://doi.org/10.1038/nmeth.2967openalex-snapshot
Bayesian approach to single-cell differential expression analysis
inferredcites →https://doi.org/10.1038/s41467-018-03751-6openalex-snapshot
Massive mining of publicly available RNA-seq data from human and mouse
inferredcites →https://doi.org/10.1038/s41467-021-21583-9openalex-snapshot
Comprehensive analysis of single cell ATAC-seq data with SnapATAC
inferredcites →https://doi.org/10.1038/s41586-018-0590-4openalex-snapshot
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
inferredcites →https://doi.org/10.1038/s41587-019-0379-5openalex-snapshot
Droplet scRNA-seq is not zero-inflated
inferredcites →https://doi.org/10.1093/bioinformatics/bth937openalex-snapshot
Robust inference of groups in gene expression time-courses using mixtures of HMMs
inferredcites →https://doi.org/10.1093/bioinformatics/btm453openalex-snapshot
Moderated statistical tests for assessing differences in tag abundance
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btu568openalex-snapshot
JAMM: a peak finder for joint analysis of NGS replicates
inferredcites →https://doi.org/10.1093/bioinformatics/bty1044openalex-snapshot
M3Drop: dropout-based feature selection for scRNASeq
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1101/gad.2005511openalex-snapshot
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
inferredcites →https://doi.org/10.1101/gr.110882.110openalex-snapshot
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
inferredcites →https://doi.org/10.1108/eb026526openalex-snapshot
A STATISTICAL INTERPRETATION OF TERM SPECIFICITY AND ITS APPLICATION IN RETRIEVAL
inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
inferredcites →https://doi.org/10.1126/science.aam8999openalex-snapshot
Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2012-13-10-r98openalex-snapshot
CHANCE: comprehensive software for quality control and validation of ChIP-seq data
inferredcites →https://doi.org/10.1186/s12859-019-2599-6openalex-snapshot
Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
inferredcites →https://doi.org/10.1186/s13059-015-0844-5openalex-snapshot
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
inferredcites →https://doi.org/10.1186/s13059-016-0938-8openalex-snapshot
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
inferredcites →https://doi.org/10.1242/dev.169854openalex-snapshot
A periodic table of cell types
inferredcites →https://doi.org/10.2202/1544-6115.1585openalex-snapshot
Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
inferredcites →https://doi.org/10.2307/3001968openalex-snapshot
Individual Comparisons by Ranking Methods
inferredcites →https://doi.org/10.32614/cran.package.matrixopenalex-snapshot
Matrix: Sparse and Dense Matrix Classes and Methods

What points at this work

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

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An in vivo neuroimmune organoid model to study human microglia phenotypes
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.109484openalex-snapshot
Tracing colonic embryonic transcriptional profiles and their reactivation upon intestinal damage
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.110251openalex-snapshot
Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors
inferred← citeshttps://doi.org/10.1016/j.devcel.2020.04.009openalex-snapshot
Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development
inferred← citeshttps://doi.org/10.1038/s41423-025-01351-1openalex-snapshot
Targeting MORF4L1-mediated DNA repair potentiates RT-induced antitumor immunity via cGAS-STING activation in hepatocellular carcinoma
inferred← citeshttps://doi.org/10.1038/s41467-020-18569-4openalex-snapshot
Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression
inferred← citeshttps://doi.org/10.1038/s41467-022-30682-0openalex-snapshot
Mapping the cardiac vascular niche in heart failure
inferred← citeshttps://doi.org/10.1038/s41467-025-64447-2openalex-snapshot
FAP+ fibroblasts orchestrate tumor microenvironment remodeling in renal cell carcinoma with tumor thrombus
inferred← citeshttps://doi.org/10.1038/s41540-024-00339-3openalex-snapshot
MarkerMap: nonlinear marker selection for single-cell studies
inferred← citeshttps://doi.org/10.1038/s41540-024-00441-6openalex-snapshot
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations
inferred← citeshttps://doi.org/10.1038/s41586-020-2941-1openalex-snapshot
Decoding myofibroblast origins in human kidney fibrosis
inferred← citeshttps://doi.org/10.1038/s41586-021-03813-8openalex-snapshot
Human neocortical expansion involves glutamatergic neuron diversification
inferred← citeshttps://doi.org/10.1038/s41586-024-08518-2openalex-snapshot
Transcriptomic neuron types vary topographically in function and morphology
inferred← citeshttps://doi.org/10.1038/s41588-022-01202-zopenalex-snapshot
Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease
inferred← citeshttps://doi.org/10.1038/s42255-021-00388-6openalex-snapshot
Mammary epithelial cells have lineage-rooted metabolic identities
inferred← citeshttps://doi.org/10.1101/2020.03.31.018820openalex-snapshot
Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons
inferred← citeshttps://doi.org/10.1101/2021.12.20.473565openalex-snapshot
Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment
inferred← citeshttps://doi.org/10.1101/2024.09.15.613138openalex-snapshot
Positional information drives distinct traits in transcriptomically identified neuronal types
inferred← citeshttps://doi.org/10.1126/sciadv.abi7640openalex-snapshot
Transcriptional census of epithelial-mesenchymal plasticity in cancer
inferred← citeshttps://doi.org/10.1186/s12859-020-03641-zopenalex-snapshot
A rank-based marker selection method for high throughput scRNA-seq data
inferred← citeshttps://doi.org/10.1186/s13059-022-02828-2openalex-snapshot
Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001032openalex-snapshot
Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis
inferred← citeshttps://doi.org/10.3390/ijms25094731openalex-snapshot
Revealing Genetic Dynamics: scRNA-seq Unravels Modifications in Human PDL Cells across In Vivo and In Vitro Environments
inferred← citeshttps://doi.org/10.3390/ijms25115617openalex-snapshot
Unraveling Divergent Transcriptomic Profiles: A Comparative Single-Cell RNA Sequencing Study of Epithelium, Gingiva, and Periodontal Ligament Tissues
inferred← citeshttps://doi.org/10.7554/elife.101918openalex-snapshot
Identification and characterization of early human photoreceptor states and cell-state-specific retinoblastoma-related features
inferred← citeshttps://doi.org/10.7554/elife.101918.2openalex-snapshot
Identification and characterization of early human photoreceptor states and cell-state-specific retinoblastoma-related features
inferred← citeshttps://doi.org/10.7554/elife.101918.3openalex-snapshot
Identification and characterization of early human photoreceptor states and cell-state-specific retinoblastoma-related features
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