DeepFun – Tissue and Cell Type specific Deep Learning Sequence-based model to Decipher Noncoding Variant Effects.

DeepFun

:: DESCRIPTION

DeepFun is a deep-learning-based model for functional evaluation of genetic variants at the single-base resolution.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Pei G, Hu R, Jia P, Zhao Z.
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner.
Nucleic Acids Res. 2021 Jul 2;49(W1):W131-W139. doi: 10.1093/nar/gkab429. PMID: 34048560; PMCID: PMC8262726.

cellassign v0.99.2 – Automated, Probabilistic Assignment of Cell Types in scRNA-seq data

cellassign v0.99.2

:: DESCRIPTION

cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

cellassign

:: MORE INFORMATION

Citation

Zhang AW, etc.
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling,
Nat Methods. 2019 Oct;16(10):1007-1015. doi: 10.1038/s41592-019-0529-1.

GiniClust3 1.0.1 – Detecting Rare Cell Types from Single-cell Gene Expression data with Gini Index

GiniClust 3 1.0.1

:: DESCRIPTION

GiniClust is a clustering method specifically designed for rare cell type detection. It uses the Gini index to identify genes that are associated with rare cell types without prior knowledge.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX
Python

:: DOWNLOAD

GiniClust

:: MORE INFORMATION

Citation

Rui Dong. Guo-Cheng Yuan.
GiniClust3: a fast and memory-efficient tool for rare cell type identification.

Genome Biol, 17 (1), 144 2016 Jul 1
GiniClust: Detecting Rare Cell Types From Single-Cell Gene Expression Data With Gini Index
Lan Jiang, Huidong Chen, Luca Pinello, Guo-Cheng Yuan

Tsoucas D, Yuan GC.
GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection.
Genome Biology. 2018 May 10;19(1):58.

DWLS – Cell-type Deconvolution using Single-cell RNA-sequencing data

DWLS

:: DESCRIPTION

DWLS (Dampened weighted least squares) is an estimation method for gene expression deconvolution, in which the cell-type composition of a bulk RNA-seq data set is computationally inferred.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
R

:: DOWNLOAD

DWLS

:: MORE INFORMATION

Citation

Tsoucas D, Dong R, Chen H, Zhu Q, Guo G, Yuan GC.
Accurate estimation of cell-type composition from gene expression data.
Nature Communications. 10 (1), 2975 2019 Jul 5

CIBERSORTx / CIBERSORT – Determining Cell Type Abundance and Expression from Bulk Tissues

CIBERSORTx / CIBERSORT

:: DESCRIPTION

CIBERSORTx is an analytical tool to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.

CIBERSORT is an analytical tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Determining cell type abundance and expression from bulk tissues with digital cytometry
Newman AM, et al.
Nat Biotechnol, 37 (7), 773-782 Jul 2019