scRNA-tools

C

CytoTRACE2

CytoTRACE 2 is a computational method for predicting cellular potency categories and absolute developmental potential from single-cell RNA-sequencing data

Publications: 0, Preprints: 1, Total citations: 28

Preprints
"Mapping single-cell developmental potential in health and disease with interpretable deep learning"
DOI: 10.1101/2024.03.19.585637, Citations: 28

Platform: R/Python
Code: https://github.com/digitalcytometry/cytotrace2
starsN/A
forksN/A
last commitUnknown
License: Custom
Categories: Ordering, Stem Cells, Visualisation
Added: 2024-03-22, Updated: 2025-01-30

F

FateID

FateID is a random forests-based algorithm for the quantification of the fate biases of multipotent progenitors, i. e. the probabilities of differentiating towards particular cell lineages.

Publications: 1, Preprints: 1, Total citations: 305

Publications
"FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data"
DOI: 10.1038/nmeth.4662, Published: 2018-04-09, Citations: 303
Preprints
"FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data"
DOI: 10.1101/218115, Citations: 2

Platform: R
Code: https://github.com/dgrun/FateID
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Classification, Differential Expression, Stem Cells, Visualisation
Added: 2017-11-21, Updated: 2021-04-16

FitDevo

FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight

Publications: 1, Preprints: 0, Total citations: 4

Publications
"FitDevo: accurate inference of single-cell developmental potential using sample-specific gene weight"
DOI: 10.1093/bib/bbac293, Published: 2022-07-24, Citations: 4

Platform: R
Code: https://github.com/jumphone/fitdevo
starsN/A
forksN/A
last commitUnknown
Categories: Ordering, Stem Cells, Visualisation
Added: 2022-08-19, Updated: 2022-08-19

H

hscScore

A method for identifying haematopoietic stem cells (HSCs) in scRNA-seq data

Publications: 1, Preprints: 0, Total citations: 44

Publications
"Machine learning predicts putative haematopoietic stem cells within large single-cell transcriptomics datasets"
DOI: 10.1016/j.exphem.2019.08.009, Published: 2019-10, Citations: 44

Platform: Python
Code: https://github.com/fionahamey/hscScore
starsN/A
forksN/A
last commitUnknown
Categories: Classification, Stem Cells
Added: 2019-09-17, Updated: 2019-09-17

L

LandSCENT

LandSCENT (Landscape Single Cell Entropy) is a R-package for the analysis of single-cell RNA-Seq data
Platform: R
Code: https://github.com/ChenWeiyan/LandSCENT
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Dimensionality Reduction, Gene Networks, Ordering, Stem Cells, Visualisation
Added: 2019-05-31, Updated: 2019-05-31

R

RaceID

RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.

Publications: 4, Preprints: 1, Total citations: 1716

Publications
"De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data"
DOI: 10.1016/j.stem.2016.05.010, Published: 2016-08, Citations: 525
"Single-cell messenger RNA sequencing reveals rare intestinal cell types"
DOI: 10.1038/nature14966, Published: 2015-08-19, Citations: 1095
"Revealing dynamics of gene expression variability in cell state space"
DOI: 10.1038/s41592-019-0632-3, Published: 2019-11-18, Citations: 79
"VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells"
DOI: 10.1186/s13059-023-02974-1, Published: 2023-06-23, Citations: 12
Preprints
"Gene expression noise dynamics unveil functional heterogeneity of ageing hematopoietic stem cells"
DOI: 10.1101/2022.08.04.502776, Citations: 5

Platform: R/C++
Code: https://github.com/dgrun/RaceID3_StemID2_package
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Clustering, Differential Expression, Dimensionality Reduction, Expression Patterns, Imputation, Integration, Marker Genes, Ordering, Rare Cells, Stem Cells, Visualisation
Added: 2016-09-09, Updated: 2023-07-14

S

scCancer

The scCancer package focuses on processing and analyzing droplet-based scRNA-seq data for cancer research. Except basic data processing steps, this package takes several special considerations for cancer-specific features.

Publications: 1, Preprints: 1, Total citations: 56

Publications
"scCancer: a package for automated processing of single-cell RNA-seq data in cancer"
DOI: 10.1093/bib/bbaa127, Published: 2020-07-06, Citations: 53
Preprints
"scCancer: a package for automated processing of single cell RNA-seq data in cancer"
DOI: 10.1101/800490, Citations: 3

Platform: R
Code: https://github.com/wguo-research/scCancer
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Cell Cycle, Classification, Clustering, Differential Expression, Gene Networks, Quality Control, Stem Cells
Added: 2019-10-30, Updated: 2019-10-30

scCancer2

An updated our R toolkit, scCancer, based on massive single-cell transcriptome and spatial transcriptome data

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

Publications
"scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution"
DOI: 10.1093/bioinformatics/btae028, Published: 2024-01-18, Citations: 0
Preprints
"scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution"
DOI: 10.1101/2023.08.22.554137, Citations: 0

Platform: R
Code: https://github.com/czythu/scCancer
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Cell Cycle, Clustering, Gene Networks, Integration, Stem Cells, Visualisation
Added: 2023-08-24, Updated: 2024-05-06

SCENT

scent is an R-package for analysis of single-cell RNA-Seq data. It uses single-cell entropy to help analyse and interpret such data.

Publications: 2, Preprints: 1, Total citations: 288

Publications
"Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome"
DOI: 10.1038/ncomms15599, Published: 2017-06-01, Citations: 264
"Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data"
DOI: 10.1093/bioinformatics/btaa987, Published: 2020-11-27, Citations: 22
Preprints
"Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome"
DOI: 10.1101/084202, Citations: 2

Platform: R
Code: https://github.com/aet21/SCENT
starsN/A
forksN/A
last commitUnknown
License: GPL-3.0
Categories: Ordering, Stem Cells
Added: 2016-11-09, Updated: 2020-12-13

Spectre

Spectre is an R package and computational toolkit that enables comprehensive end-to-end integration, exploration, and analysis of high-dimensional cytometry, imaging, or single-cell data from different batches or experiments

Publications: 1, Preprints: 1, Total citations: 125

Publications
"Integration, exploration, and analysis of high‐dimensional single‐cell cytometry data using Spectre"
DOI: 10.1002/cyto.a.24350, Published: 2021-04-26, Citations: 117
Preprints
"Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre"
DOI: 10.1101/2020.10.22.349563, Citations: 8

Platform: R
Code: https://github.com/ImmuneDynamics/Spectre
starsN/A
forksN/A
last commitUnknown
License: MIT
Categories: Classification, Clustering, Differential Expression, Dimensionality Reduction, Expression Patterns, Immune, Integration, Marker Genes, Normalisation, Ordering, Quality Control, Rare Cells, Stem Cells
Added: 2021-11-05, Updated: 2021-11-05

Tools

View entries for individual tools

Sorting & Filters

C

CytoTRACE2

Preprints

F

FateID

Publications

Preprints

FitDevo

Publications

H

hscScore

Publications

L

LandSCENT

R

RaceID

Publications

Preprints

S

scCancer

Publications

Preprints

scCancer2

Publications

Preprints

SCENT

Publications

Preprints

Spectre

Publications

Preprints