S-Mart 1.1.4 – Aid RNA-seq Data Analysis

S-Mart 1.1.4

:: DESCRIPTION

S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

::DEVELOPER

URGI

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Java
Python

:: DOWNLOAD

S-Mart

:: MORE INFORMATION

Citation

Matthias Zytnicki
S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
PLoS One. 2011; 6(10): e25988.

ChangePoint 0.1.1 – Change-point model for detecting 3’UTR Changes by RNA-Seq

ChangePoint 0.1.1

:: DESCRIPTION

ChangePoint is a change-point model based on a likelihood ratio test for detecting 3’UTR switching.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

ChangePoint

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 11. pii: btu189. [Epub ahead of print]
A change-point model for identifying 3’UTR switching by next-generation RNA sequencing.
Wang W, Wei Z, Li H.

BreakFusion 1.0.1 – Identify Gene Fusions from paired-end RNA-Seq data

BreakFusion 1.0.1

:: DESCRIPTION

BreakFusion is a software that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

BreakFusion

:: MORE INFORMATION

Citation:

Ken Chen et al.
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Bioinformatics (2012) 28 (14): 1923-1924.

GIIRA 01_3 – RNA-Seq driven Gene Finding Incorporating Ambiguous Reads

GIIRA 01_3

:: DESCRIPTION

GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment.

::DEVELOPER

Bernhard Y. Renard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java
Python

:: DOWNLOAD

GIIRA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):606-13. doi: 10.1093/bioinformatics/btt577. Epub 2013 Oct 11.
GIIRA–RNA-Seq driven gene finding incorporating ambiguous reads.
Zickmann F1, Lindner MS, Renard BY.

R-SAP 1.1 – RNA-Seq Analysis pipeline

R-SAP 1.1

:: DESCRIPTION

R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values.

::DEVELOPER

McDonald Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Perl

:: DOWNLOAD

R-SAP

:: MORE INFORMATION

Citation:

Mittal VK, McDonald JF. 2012.
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.
Nucleic Acid Reseaech. Jan. 28;

scRNABatchQC v0.10.3 – multi-samples Quality Control for single cell RNA-seq data

scRNABatchQC v0.10.3

:: DESCRIPTION

scRNABatchQC is an R package for generating a HTML QC report to check and compare quality of multiple single cell RNA-seq datasets. scRNABatchQC supports multiple types of inputs, including gene-cell count matrices, 10x genomics, SingleCellExperiment or Seurat v3 objects.

::DEVELOPER

scRNABatchQC team

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

scRNABatchQC

:: MORE INFORMATION

Citation

Liu Q, Sheng Q, Ping J, Ramirez MA, Lau KS, Coffey RJ, Shyr Y.
scRNABatchQC: multi-samples quality control for single cell RNA-seq data.
Bioinformatics. 2019 Dec 15;35(24):5306-5308. doi: 10.1093/bioinformatics/btz601. PMID: 31373345; PMCID: PMC6954654.

Yanagi – Segment-based RNA-seq analysis

Yanagi

:: DESCRIPTION

Yanagi is a tool which segments a transcriptome into disjoint regions to create a segments library from a complete transcriptome annotation that preserves all of its consecutive regions of a given length L while distinguishing annotated alternative splicing events in the transcriptome.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
R
Python

:: DOWNLOAD

Yanagi

:: MORE INFORMATION

Citation

Gunady MK, Mount SM, Corrada Bravo H.
Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis.
BMC Bioinformatics. 2019 Aug 13;20(1):421. doi: 10.1186/s12859-019-2947-6. PMID: 31409274; PMCID: PMC6693274.

consexpression – Tool for RNA-Seq analysis

consexpression

:: DESCRIPTION

The consexpression approach is a pipeline for expression analysis that adopts the identification of DEGs from the joint analysis of nine tools.

::DEVELOPER

consexpression team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows /Linux / MacOs
R
Python

:: DOWNLOAD

consexpression

:: MORE INFORMATION

Citation:

Costa-Silva J, Domingues D, Lopes FM.
RNA-Seq differential expression analysis: An extended review and a software tool.
PLoS One. 2017 Dec 21;12(12):e0190152. doi: 10.1371/journal.pone.0190152. PMID: 29267363; PMCID: PMC5739479.

AltAnalyze 2.1.4.3 – Microarry and RNA-Seq Analysis

AltAnalyze 2.1.4.3

:: DESCRIPTION

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

::DEVELOPER

the Nathan Salomonis laboratory at Cincinnati Children’s Hosptial Medical Center and the University of Cincinnati.

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux / MacOsX
Python

:: DOWNLOAD

AltAnalyze

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W755-62. Epub 2010 May 31.
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M.

netSmooth v0.1.0 – A Network smoothing based method for single cell RNA-seq

netSmooth v0.1.0

:: DESCRIPTION

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using gene interaction networks such as protein- protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNA-seq data.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R
BioConductor

:: DOWNLOAD

netSmooth

:: MORE INFORMATION

Citation

Ronen J, Akalin A.
netSmooth: Network-smoothing based imputation for single cell RNA-seq.
F1000Res. 2018 Jan 3;7:8. doi: 10.12688/f1000research.13511.3. PMID: 29511531; PMCID: PMC5814748.