MAP-RSeq 1.2.1 – System for RNA-Sequencing Data Analysis

MAP-RSeq 1.2.1

:: DESCRIPTION

MAP-RSeq ( The Mayo Analysis Pipeline for RNA Seq) is comprehensive system for RNA-Sequencing data analysis. The MAP-RSeq workflow integrates a suite of open source bioinformatics tools along with in-house developed methods to analyze paired-end RNA-Seq data.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MAP-RSeq

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 27;15:224. doi: 10.1186/1471-2105-15-224.
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Kalari KR, Nair AA, Bhavsar JD, O’Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP

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

RESCUE v1.0.3 – Imputing Dropouts in Single-cell RNA-sequencing data

RESCUE v1.0.3

:: DESCRIPTION

RESCUE is a computational method to mitigate the dropout problem by imputing gene expression levels using information from other cells with similar patterns.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python
  • R

:: DOWNLOAD

RESCUE

:: MORE INFORMATION

Citation

BMC Bioinformatics, 20 (1), 388 2019 Jul 12
RESCUE: Imputing Dropout Events in Single-Cell RNA-sequencing Data
Sam Tracy , Guo-Cheng Yuan , Ruben Dries

VirtualCytometry – Webserver for the Study of Immune Cell Differentiation using single-cell RNA sequencing data

VirtualCytometry

:: DESCRIPTION

VirtualCytometry is a webserver that provides computational platform for the study of immune cell differentiation using scRNA-seq data by enabling identification and validation of genes involved in immune cell differentiations via ‘Discovery Module’ and ‘Hypothesis Test Module’ respectively.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Aug 2. pii: btz610. doi: 10.1093/bioinformatics/btz610.
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data.
Kim K, Yang S, Ha SJ, Lee I.

PLNseq 1.0 – Poisson Lognormal Distribution for High-throughput matched RNA-sequencing Read Count data

PLNseq 1.0

:: DESCRIPTION

The PLNseq package conducts differential expression (DE) analysis using high throughput  RNA-seq read count data generated from correlated samples.

::DEVELOPER

Hong Zhang @Fudan University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

PLNseq

:: MORE INFORMATION

Citation

Stat Med. 2015 Apr 30;34(9):1577-89. doi: 10.1002/sim.6449. Epub 2015 Jan 30.
PLNseq: a multivariate Poisson lognormal distribution for high-throughput matched RNA-sequencing read count data.
Zhang H1, Xu J, Jiang N, Hu X, Luo Z.

ALEXA-Seq 1.17 – Alternative Expression Analysis by massively parallel RNA Sequencing

ALEXA-Seq 1.17

:: DESCRIPTION

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for ‘alternative expression analysis’.

::DEVELOPER

ALEXA-Seq Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Virtual Machines

:: DOWNLOAD

 ALEXA-Seq

:: MORE INFORMATION

Citation:

Malachi Griffith, et al.
Alternative expression analysis by RNA sequencing.
Nature Methods. 2010 Oct;7(10):843-847.