Quantas 1.0.9 – Analyze alternative Splicing using RNA-Seq

Quantas 1.0.9

:: DESCRIPTION

Quantas includes a package to infer transcript structure from paired-end RNA-seq data (gapless), and a package to count RNA-seq reads for each alternative splicing isoform (countit).

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl 

:: DOWNLOAD

 Quantas

:: MORE INFORMATION

mRIN 1.2.0 – direct Assessment of mRNA integrity from RNA-Seq data

mRIN 1.2.0

:: DESCRIPTION

mRIN (mRNA integrity number) is a computational method to assess a quantitative measure of mRNA integrityta. This is done by quantitatively modeling of the 3′ bias of read coverage profiles along each mRNA transcript. A per-sample summary mRIN is then derived as an indicator of mRNA degradation. This method has been used for systematic analysis of large scale RNA-Seq data of postmortem tissues, in which RNA degradation during tissue collection is particularly an issue.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl 

:: DOWNLOAD

mRIN

:: MORE INFORMATION

Citation

Nat Commun. 2015 Aug 3;6:7816. doi: 10.1038/ncomms8816.
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.
Feng H, Zhang X, Zhang C

dSpliceType 2.0.0 – Detect various types of differential Splicing Events using RNA-Seq

dSpliceType 2.0.0

:: DESCRIPTION

dSpliceType is a fast, effective and accurate computational method to detect various types of differential splicing and differential expression events between two conditions using RNA-Seq

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

dSpliceType

:: MORE INFORMATION

Citation:

A generalized dSpliceType framework to detect differential splicing and differential expression events using RNA-Seq.
Zhu D, Deng N, Bai C.
IEEE Trans Nanobioscience. 2015 Mar;14(2):192-202. doi: 10.1109/TNB.2015.2388593.

SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis

SAMMate 2.7.4 / assemblySAM 1.1

:: DESCRIPTION

SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

sammate

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • R package

:: DOWNLOAD

 SAMMate / assemblySAM

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G1, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Nguyen, T, Zhao, Z, Zhu, D.
SPATA: A seeding and patching algorithm for hybrid transcriptome assembly.

Nguyen, T, Deng, N, Zhu, D.
SASeq: A selective and adaptive shrinkage approach to detect and quantify active transcripts using RNA-Seq.

TrueSight 0.06 – Self-training Algorithm for Splice Junction Detection using RNA-seq

TrueSight 0.06

:: DESCRIPTION

TrueSight is a self-training algorithm for splice junction detection using RNA-seq

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TrueSight

:: MORE INFORMATION

Citation

Li Y, Li H, Burns P, Borodovsky M, Robinson GE, and Ma J.
TrueSight: self-training algorithm for splice junction detection using RNA-seq.
To appear in Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2012.

TRUST4 v0.1.1 – TCR and BCR Assembly from RNA-seq data

TRUST4 v0.1.1

:: DESCRIPTION

TRUST (T cell receptor Repertoire Utilities for Solid Tissue/Tumor) is a toolbox for analyzing T cell receptors in solid tumors using unselected RNA-seq data based on de novo assembly.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRUST

:: MORE INFORMATION

 

GFold 1.1.4 – Generalized fold change for Rank Differentially Expressed Genes from RNA-seq data

GFold 1.1.4

:: DESCRIPTION

gfold (Generalized fold change) generalizes the fold change by considering the posterior distribution of log fold change, such that each gene is assigned a reliable fold change. It overcomes the shortcoming of p-value that measures the significance of whether a gene is differentially expressed under different conditions instead of measuring relative expression changes, which are more interesting in many studies. It also overcomes the shortcoming of fold change that suffers from the fact that the fold change of genes with low read count are not so reliable as that of genes with high read count, even these two genes show the same fold change.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GFold

:: MORE INFORMATION

Citation

Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y.
GFOLD: a generalized fold change for ranking differentially ex-pressed genes from RNA-seq data.
Bioinformatics (2012) 28 (21): 2782-2788.

rlsim 1.4 – Simulating RNA-seq library Preparation with Parameter Estimation

rlsim 1.4

:: DESCRIPTION

The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Biopython

:: DOWNLOAD

  rlsim

:: MORE INFORMATION

Citation:

Botond Sipos, Tim Massingham and Nick Goldman (2013):
rlsim – a package for simulating RNA-seq library preparation with parameter estimation.
http://bit.ly/rlsim-doc

Epi-Seq 1.0.0 – Predicting Tumor Specific Epitopes from RNA-Seq data

Epi-Seq 1.0.0

:: DESCRIPTION

Epi-Seq is a multi-step bioinformatics analysis pipeline that starts from the raw RNA-Seq tumor reads, and produces a set of predicted tumor-specific expressed epitopes.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Epi-Seq

:: MORE INFORMATION

SC1 – A web-based Single Cell RNA-seq Analysis Pipeline

SC1

:: DESCRIPTION

SC1 is a web-based single cell RNA-seq analysis pipeline.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

J Comput Biol. 2019 Aug;26(8):822-835. doi: 10.1089/cmb.2018.0236. Epub 2019 Feb 19.
Locality Sensitive Imputation for Single Cell RNA-Seq Data.
Moussa M, Măndoiu II.