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A

anchor

Find bimodal, unimodal, and multimodal features in your data

Publications: 1, Preprints: 0, Total citations: 171

Publications
"Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation"
DOI: 10.1016/j.molcel.2017.06.003, Published: 2017-07, Citations: 171

Platform: Python
Code: https://github.com/yeolab/anchor
starsN/A
forksN/A
last commitUnknown
License: BSD-3-Clause
Categories: Modality
Added: 2016-09-08, Updated: 2017-07-16

D

DESCEND

DESCEND deconvolves the true gene expression distribution across cells for UMI scRNA-seq counts

Publications: 1, Preprints: 1, Total citations: 84

Publications
"Gene expression distribution deconvolution in single-cell RNA sequencing"
DOI: 10.1073/pnas.1721085115, Published: 2018-06-26, Citations: 78
Preprints
"Gene Expression Distribution Deconvolution in Single Cell RNA Sequencing"
DOI: 10.1101/227033, Citations: 6

Platform: R
Code: https://github.com/jingshuw/descend
starsN/A
forksN/A
last commitUnknown
License: GPL-2.0-or-later
Categories: Differential Expression, Modality, Variable Genes, Visualisation
Added: 2017-12-20, Updated: 2017-12-20

L

LTMGSCA

LTMGSCA is a left truncated mixture Gaussian (LTMG) model-based single cell RNA-seq analysis pipeline that can accurately infer the modality and distribution of individual gene’s expression profile in scRNA-seq data, while decrease the impact from dropout and low expression value.

Publications: 1, Preprints: 1, Total citations: 47

Publications
"LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data"
DOI: 10.1093/nar/gkz655, Published: 2019-08-02, Citations: 47
Preprints
"LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data"
DOI: 10.1101/430009, Citations: 0

Platform: R
Code: https://github.com/clwan/LTMGSCA
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Clustering, Differential Expression, Dimensionality Reduction, Modality, Transformation, Visualisation
Added: 2019-08-12, Updated: 2020-04-29

M

M3S

M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data

Publications: 1, Preprints: 0, Total citations: 6

Publications
"M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data"
DOI: 10.1186/s12859-019-3243-1, Published: 2019-12-20, Citations: 6

Platform: R
Code: https://github.com/zy26/M3S
starsN/A
forksN/A
last commitUnknown
License: CC-BY-NC-ND-4.0
Categories: Modality
Added: 2020-01-02, Updated: 2020-01-02

S

Scanpro

Scanpro is a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the python environment

Publications: 1, Preprints: 2, Total citations: 6

Publications
"Scanpro is a tool for robust proportion analysis of single-cell resolution data"
DOI: 10.1038/s41598-024-66381-7, Published: 2024-07-06, Citations: 5
Preprints
"Scanpro: robust proportion analysis for single cell resolution data"
DOI: 10.1101/2023.08.14.553234, Citations: 1
"Scanpro: robust proportion analysis for single cell resolution data"
DOI: 10.21203/rs.3.rs-3375942/v1, Citations: 0

Platform: Python
Code: https://github.com/loosolab/scanpro
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Modality
Added: 2023-08-18, Updated: 2025-04-13

scCODA

scCODA allows for identification of compositional changes in high-throughput sequencing count data, especially cell compositions from scRNA-seq

Publications: 1, Preprints: 1, Total citations: 243

Publications
"scCODA is a Bayesian model for compositional single-cell data analysis"
DOI: 10.1038/s41467-021-27150-6, Published: 2021-11-25, Citations: 231
Preprints
"scCODA: A Bayesian model for compositional single-cell data analysis"
DOI: 10.1101/2020.12.14.422688, Citations: 12

Platform: Python
Code: https://github.com/theislab/scCODA
starsN/A
forksN/A
last commitUnknown
License: BSD-3-Clause
Categories: Modality
Added: 2021-01-08, Updated: 2021-11-27

SDAMS

Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data
Platform: R
Code: https://bioconductor.org/packages/SDAMS
License: GPL-1.0
Categories: Modality
Added: 2021-08-06, Updated: 2021-08-06

T

tascCODA

Tree-aggregated compositional analysis for high-throughput sequencing data

Publications: 1, Preprints: 1, Total citations: 10

Publications
"tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data"
DOI: 10.3389/fgene.2021.766405, Published: 2021-12-07, Citations: 9
Preprints
"tascCODA: Bayesian tree-aggregated analysis of compositional amplicon and single-cell data"
DOI: 10.1101/2021.09.06.459120, Citations: 1

Platform: Python
Code: https://github.com/bio-datascience/tascCODA
starsN/A
forksN/A
last commitUnknown
License: BSD-3-Clause
Categories: Modality
Added: 2021-09-10, Updated: 2021-12-17