ImmuCellAI / ImmuCellAI-mouse – Immune Cell Abundance Identifier / for mouse

ImmuCellAI / ImmuCellAI-mouse

:: DESCRIPTION

ImmuCellAI is a tool to estimate the abundance of 24 immune cells from gene expression dataset including RNA-Seq and microarray data, in which the 24 immune cells are comprised of 18 T-cell subtypes and 6 other immune cells: B cell, NK cell, Monocyte cell, Macrophage cell, Neutrophil cell and DC cell.

ImmuCellAI-mouse is the mouse version of ImmuCellAI. ImmuCellAI-mouse is a tool to estimate the abundance of 36 immune cells based on gene expression profile from RNA-Seq or microarray data. To ensure the prediction accuracy, we adopted a hierarchical strategy to classify the 36 cell types into three layers, which were presented as inclusion relation among different circles in the right figure.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Miao YR, Xia M, Luo M, Luo T, Yang M, Guo AY.
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction.
Bioinformatics. 2021 Oct 12:btab711. doi: 10.1093/bioinformatics/btab711. Epub ahead of print. PMID: 34636837.

Miao YR, Zhang Q, Lei Q, Luo M, Xie GY, Wang H, Guo AY.
ImmuCellAI: A Unique Method for Comprehensive T-Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy.
Adv Sci (Weinh). 2020 Feb 11;7(7):1902880. doi: 10.1002/advs.201902880. PMID: 32274301; PMCID: PMC7141005.

FastViromeExplorer – Virus and Phage Identification and Abundance profiling in Metagenomics data

FastViromeExplorer

:: DESCRIPTION

FastViromeExplorer is a stand-alone pipeline for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Java

:: DOWNLOAD

FastViromeExplorer

:: MORE INFORMATION

Citation

Tithi SS, Aylward FO, Jensen RV, Zhang L.
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.
PeerJ. 2018 Jan 12;6:e4227. doi: 10.7717/peerj.4227. PMID: 29340239; PMCID: PMC5768174.

PseudoLasso v2 – Efficient approach to correct Read Alignment for Pseudogene Abundance Estimates

PseudoLasso v2

:: DESCRIPTION

PseudoLasso is a linear regression approach to learn read alignment behaviors, and to leverage this knowledge for abundance estimation and alignment correction.

::DEVELOPER

Wei Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Python

:: DOWNLOAD

PseudoLasso

:: MORE INFORMATION

Citation

Ju CJ, Zhao Z, Wang W.
Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates.
IEEE/ACM Trans Comput Biol Bioinform. 2017 May-Jun;14(3):522-533. doi: 10.1109/TCBB.2016.2591533. Epub 2016 Jul 14. PMID: 27429446; PMCID: PMC5514313.

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

AbundanceBin 1.0.1 – Abundance-based tool for Binning Metagenomic Sequences

AbundanceBin 1.0.1

:: DESCRIPTION

AbundanceBin is an abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes—-two important characteristic parameters for a microbial community.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AbundanceBin

:: MORE INFORMATION

Citation:

Yu-Wei Wu and Yuzhen Ye.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010)