ComiR 20151020 – Combinatorial miRNA target prediction tool

ComiR 20151020

:: DESCRIPTION

ComiR (Combinatorial miRNA targeting) predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

C. Coronnello, R. Hartmaier, A. Arora, L. Huleihel, K.V. Pandit, A.S Bais, M. Butterworth, N. Kaminski, G.D. Stormo, S. Oesterreich, P.V. Benos (2012),
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density,
PLoS Comput Bio 8(12): e1002830. doi:10.1371/journal.pcbi.1002830

RNAenn – Energy Parameters and novel algorithms for Extended nearest Neighbor Energy Model of RNA

RNAenn

:: DESCRIPTION

RNAenn computes the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model.

::DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAenn

:: MORE INFORMATION

Citation

Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.
Dotu I, Mechery V, Clote P.
PLoS One. 2014 Feb 21;9(2):e85412. doi: 10.1371/journal.pone.0085412.

BASIS v1 – Bayesian Analysis of Splicing IsoformS

BASIS v1

:: DESCRIPTION

BASIS is a software tool to identify differentially expressed transcript isoforms from high-throughput RNA-seq data or high-density tiling arrays.

:: DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BASIS

:: MORE INFORMATION

Citation:

Sika Zheng and Liang Chen
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
Nucleic Acids Research 37(10):e75 (2009)

WemIQ – Isoform Quantification method for RNA-seq data

WemIQ

:: DESCRIPTION

WemIQ is a software tool to quantify isoform expression and exon splicing ratios from RNA-seq data accurately and robustly.

::DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WemIQ

:: MORE INFORMATION

Citation

WemIQ: An accurate and robust isoform quantification method for RNA-seq data.
Zhang J, Kuo CC, Chen L.
Bioinformatics. 2014 Nov 17. pii: btu757.

GPSeq 0.5 – Using the Generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments

GPSeq 0.5

:: DESCRIPTION

GPSeq is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.

:: DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package/Perl/C Compiler

:: DOWNLOAD

 GPSeq

:: MORE INFORMATION

Citation:

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Srivastava S, Chen L.
Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670.

EBChangePoint 0.1.0 – Empirical Bayes Change-point Model

EBChangePoint 0.1.0

:: DESCRIPTION

EBChangePoint could efficiently pool information across genes to improve detection efficiency.

::DEVELOPER

EBChangePoint team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 EBChangePoint

:: MORE INFORMATION

Citation:

An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing.
Zhang J, Wei Z.
Bioinformatics. 2016 Feb 11. pii: btw060.

DaPars 0.9.1 – Dynamic analysis of Alternative PolyAdenylation from RNA-seq

DaPars 0.9.1

:: DESCRIPTION

DaPars is a novel bioinformatics algorithm for the de novo identification of dynamic APAs from standard RNA-seq.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DaPars

:: MORE INFORMATION

Citation:

Xia, Z., Donehower, L.A., Wheeler, D.A., Cooper, T.A., Neilson, J.R., Wagner E.J., Li, W. 2014.
Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types.
Nature Communications, 5:5274.

CPAT 2.0.0 – RNA Coding Potential Assessment Tool

CPAT 2.0.0

:: DESCRIPTION

CPAT (Coding Potential Assessment Tool) is a novel alignment-free method which rapidly recognizes coding and noncoding transcripts from a large pool of candidates.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R package

:: DOWNLOAD

 CPAT

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006. Epub 2013 Jan 17.
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.
Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W.

RSeQC v3.0.1 – RNA-seq Quality Control package

RSeQC v3.0.1

:: DESCRIPTION

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 RSeQC

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27.
RSeQC: quality control of RNA-seq experiments.
Wang L, Wang S, Li W.

riboPicker 0.4.3 – Identification and Removal of rRNA-like Sequences.

riboPicker 0.4.3

:: DESCRIPTION

riboPicker is a tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too.

riboPicker Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 riboPicker

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Feb 1;28(3):433-5. Epub 2011 Dec 6.
Identification and removal of ribosomal RNA sequences from metatranscriptomes.
Schmieder R, Lim YW, Edwards R.