Tag: RNA-Seq

VERSE v1.0.5 – Versatile and Efficient RNA-Seq Read Counting Tool

VERSE v1.0.5

:: DESCRIPTION

VERSE is designed for high-performance read summarization for next generation sequencing. VERSE is 50x faster than HTSeq when computing the same gene counts. It introduces a novel, hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. There is also a set of parameters the user can use to fine-tune the assignment logic. VERSE can be readily incorporated into any existing RNA-Seq analysis pipelines.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

VERSE 

:: MORE INFORMATION

Citation

Zhu, Q., Fisher, S.A., Shallcross, J., Kim, J. (Preprint).
VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv 053306.
doi: http://dx.doi.org/10.1101/053306

asSeq 0.99.2 – Statistical Framework for eQTL Mapping using RNA-seq Data

asSeq 0.99.2

:: DESCRIPTION

asSeq is a software of allele specific study of next generation sequencing data, with emphasis on RNA-seq and ChIP-seq data.

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 asSeq

:: MORE INFORMATION

Citation

Sun W.
A Statistical Framework for eQTL Mapping Using RNA-seq Data.
Biometrics. 2011 Aug 12.

Trinity 2.13.2 – RNA-Seq De novo Assembly

Trinity 2.13.2

:: DESCRIPTION

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Java

:: DOWNLOAD

Trinity

:: MORE INFORMATION

Citation

Manfred G. Grabherr, Brian J. Haas, […], and Aviv Regev
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Nat Biotechnol. 2011 May 15; 29(7): 644–652. doi: 10.1038/nbt.1883

VARUS 1.0.0 – Drawing Diverse Samples from RNA-Seq Libraries

VARUS 1.0.0

:: DESCRIPTION

VARUS automates the selection and download of a limited number of RNA-seq reads from at NCBI’s Sequence Read Archive (SRA) targeting a sufficiently high coverage for many genes for the purpose of gene-finder training and genome annotation.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VARUS

:: MORE INFORMATION

Citation

Stanke M, Bruhn W, Becker F, Hoff KJ.
VARUS: sampling complementary RNA reads from the sequence read archive.
BMC Bioinformatics. 2019 Nov 8;20(1):558. doi: 10.1186/s12859-019-3182-x. PMID: 31703556; PMCID: PMC6842140.

NorahDesk 1.4 – Detecting small non-coding RNA(ncRNA) from Deep Sequencing data (RNA-seq)

NorahDesk 1.4

:: DESCRIPTION

NorahDesk is a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data. NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes.

::DEVELOPER

NorahDesk team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Vienna RNA

:: DOWNLOAD

 NorahDesk

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep;40(16):7633-43. doi: 10.1093/nar/gks505.
Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.
Ragan C, Mowry BJ, Bauer DC.

Grape 1.1.0 – Pipeline for Processing and Analyzing RNA-Seq data

Grape 1.1.0

:: DESCRIPTION

The Grape RNAseq Analysis Pipeline Environment implements a set of workflows that allow for easy exploration of RNA-Seq data.

::DEVELOPER

Guigo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Grape

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Mar 1;29(5):614-21. doi: 10.1093/bioinformatics/btt016. Epub 2013 Jan 17.
Grape RNA-Seq analysis pipeline environment.
Knowles DG, Röder M, Merkel A, Guigó R.

MIDAS – MIning Differentially Activated Subpaths of KEGG pathways from multi-class RNA-seq data

MIDAS

:: DESCRIPTION

MIDAS is an algorithm that determines condition specific subpaths, each of which has different activities across multiple phenotypes. MIDAS utilizes gene expression quantity information fully and the network centrality information to determine condition specific subpaths.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

MIDAS

:: MORE INFORMATION

Citation

Lee S, Park Y, Kim S.
MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data.
Methods. 2017 Jul 15;124:13-24. doi: 10.1016/j.ymeth.2017.05.026. Epub 2017 Jun 1. PMID: 28579402.

TRAP 2.3 – Time-series RNA-seq Analysis Package

TRAP 2.3

:: DESCRIPTION

TRAP is a package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRAP

:: MORE INFORMATION

Citation

Jo K, Kwon HB, Kim S.
Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress.
Methods. 2014 Jun 1;67(3):364-72. doi: 10.1016/j.ymeth.2014.02.001. Epub 2014 Feb 8. PMID: 24518221.

SpliceHetero – Measuring Spliceomic Intratumor Heterogeneity from bulk-tumor RNA-seq

SpliceHetero

:: DESCRIPTION

SpliceHetero is a novel computational method to measure spliceome level intra-tumor heterogeneity (sITH) in breast cancer.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SpliceHetero

:: MORE INFORMATION

Citation

Kim M, Lee S, Lim S, Kim S.
SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq.
PLoS One. 2019 Oct 23;14(10):e0223520. doi: 10.1371/journal.pone.0223520. PMID: 31644551; PMCID: PMC6808416.

DegPack – Identifying DEGs in multiclass RNA-seq data

DegPack

:: DESCRIPTION

DegPack is a web package using a non-parametric and information theoretic algorithm to identify differentially expressed genes in multiclass RNA-seq samples.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

 DegPack

:: MORE INFORMATION

Citation

Methods. 2014 Oct 1;69(3):306-14. doi: 10.1016/j.ymeth.2014.06.004. Epub 2014 Jun 26.
DegPack: a web package using a non-parametric and information theoretic algorithm to identify differentially expressed genes in multiclass RNA-seq samples.
An J, Kim K, Chae H, Kim S