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CONFESS: Fluorescence-based single-cell ordering in R

https://doi.org/10.1101/407932
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What this work says

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

inferredcites →https://doi.org/10.1002/cyto.a.21007openalex-snapshot
Rapid cell population identification in flow cytometry data
inferredcites →https://doi.org/10.1016/j.cell.2007.12.033openalex-snapshot
Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression
inferredcites →https://doi.org/10.1016/j.cell.2014.04.005openalex-snapshot
Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development
inferredcites →https://doi.org/10.1016/j.molcel.2017.10.001openalex-snapshot
Genetically Encoded Tools for Optical Dissection of the Mammalian Cell Cycle
inferredcites →https://doi.org/10.1016/j.stem.2015.07.013openalex-snapshot
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis
inferredcites →https://doi.org/10.1016/j.ymeth.2015.06.021openalex-snapshot
Computational assignment of cell-cycle stage from single-cell transcriptome data
inferredcites →https://doi.org/10.1023/a:1008981510081openalex-snapshot
Robust mixture modelling using the t distribution
inferredcites →https://doi.org/10.1038/nbt.3102openalex-snapshot
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
inferredcites →https://doi.org/10.1038/ncomms15599openalex-snapshot
Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome
inferredcites →https://doi.org/10.1038/nmeth.2645openalex-snapshot
Accounting for technical noise in single-cell RNA-seq experiments
inferredcites →https://doi.org/10.1038/nmeth.3545openalex-snapshot
Trajectories of cell-cycle progression from fixed cell populations
inferredcites →https://doi.org/10.1038/nmeth.3549openalex-snapshot
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
inferredcites →https://doi.org/10.1038/nmeth.4150openalex-snapshot
Single-cell mRNA quantification and differential analysis with Census
inferredcites →https://doi.org/10.1073/pnas.1408993111openalex-snapshot
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
inferredcites →https://doi.org/10.1089/10665270252833190openalex-snapshot
Improved Background Correction for Spotted DNA Microarrays
inferredcites →https://doi.org/10.1093/bioinformatics/btl412openalex-snapshot
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
inferredcites →https://doi.org/10.1093/bioinformatics/btm412openalex-snapshot
A comparison of background correction methods for two-colour microarrays
inferredcites →https://doi.org/10.1093/bioinformatics/btq046openalex-snapshot
EBImage—an R package for image processing with applications to cellular phenotypes
inferredcites →https://doi.org/10.1093/bioinformatics/bts300openalex-snapshot
flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding
inferredcites →https://doi.org/10.1093/bioinformatics/btw372openalex-snapshot
Pseudotime estimation: deconfounding single cell time series
inferredcites →https://doi.org/10.1093/biostatistics/kxn042openalex-snapshot
Microarray background correction: maximum likelihood estimation for the normal-exponential convolution
inferredcites →https://doi.org/10.1093/nar/gkw1278openalex-snapshot
SLICE: determining cell differentiation and lineage based on single cell entropy
inferredcites →https://doi.org/10.1093/nar/gkw430openalex-snapshot
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
inferredcites →https://doi.org/10.1093/nar/gkx949openalex-snapshot
SCPortalen: human and mouse single-cell centric database
inferredcites →https://doi.org/10.1101/088500openalex-snapshot
Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells
inferredcites →https://doi.org/10.1101/gr.161034.113openalex-snapshot
From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
inferredcites →https://doi.org/10.1111/1467-9868.00293openalex-snapshot
Estimating the Number of Clusters in a Data Set Via the Gap Statistic
inferredcites →https://doi.org/10.1111/j.1467-9876.2007.00567.xopenalex-snapshot
GOES-8 X-Ray Sensor Variance Stabilization Using the Multiscale Data-Driven Haar–Fisz Transform
inferredcites →https://doi.org/10.1186/1471-2105-11-403openalex-snapshot
Data reduction for spectral clustering to analyze high throughput flow cytometry data
inferredcites →https://doi.org/10.1186/1471-2164-3-19openalex-snapshot
Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer
inferredcites →https://doi.org/10.1186/s13059-015-0636-yopenalex-snapshot
Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment
inferredcites →https://doi.org/10.1186/s13059-015-0739-5openalex-snapshot
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells
inferredcites →https://doi.org/10.1186/s13059-016-0888-1openalex-snapshot
Classification of low quality cells from single-cell RNA-seq data
inferredcites →https://doi.org/10.1198/106186004x2697openalex-snapshot
A Haar-Fisz Algorithm for Poisson Intensity Estimation
inferredcites →https://doi.org/10.1371/journal.pone.0136964openalex-snapshot
Poisson-Gaussian Noise Reduction Using the Hidden Markov Model in Contourlet Domain for Fluorescence Microscopy Images
inferredcites →https://doi.org/10.18637/jss.v011.i08openalex-snapshot
FlexMix: A General Framework for Finite Mixture Models and Latent Class Regression in R
inferredcites →https://doi.org/10.18637/jss.v012.i08openalex-snapshot
EbayesThresh:RPrograms for Empirical Bayes Thresholding
inferredcites →https://doi.org/10.18637/jss.v019.i01openalex-snapshot
Adaptive Smoothing of Digital Images: TheRPackageadimpro
inferredcites →https://doi.org/10.18637/jss.v019.i02openalex-snapshot
Bayesian Smoothing with Gaussian Processes Using Fourier Basis Functions in thespectralGPPackage
inferredcites →https://doi.org/10.20347/wias.preprint.1177openalex-snapshot
Adaptive smoothing of digital images : the R package adimpro
inferredcites →https://doi.org/10.32614/cran.package.rasteropenalex-snapshot
raster: Geographic Data Analysis and Modeling
inferredcites →https://doi.org/10.4161/cc.8.7.8042openalex-snapshot
Quantitative analysis of cell cycle phase durations and PC12 differentiation using fluorescent biosensors

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41467-018-08126-5openalex-snapshot
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
inferred← citeshttps://doi.org/10.1101/2024.12.31.630907openalex-snapshot
Optimal Inference of Asynchronous Boolean Networks
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