ProMISe 1.24.0 – Infer miRNA-mRNA interactions using paired expression data from a single sample

ProMISe 1.24.0

:: DESCRIPTION

ProMISe is a novel approach to infer Probabilistic MiRNA-mRNA Interaction Signature from a single pair of miRNA-mRNA expression profile. Our model considers mRNA and miRNA competition as a probabilistic function of the expressed seeds (matches).

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ProMISe

:: MORE INFORMATION

Citation

Li, Y., Liang, C., Wong, KC, Jin, K., and Zhang, Z. (Feb, 2014)
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. Nucleic Acids Research
Nucl. Acids Res. (2014) doi: 10.1093/nar/gku182

RIPSeeker 1.26.0 – de novo RIP Peak Predictions based on HMM.

RIPSeeker 1.26.0

:: DESCRIPTION

RIPSeeker is a free open-source Bioconductor/R package for identifying protein-associated transcripts from RIP-seq experiments.

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 RIPSeeker

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Li Y1, Zhao DY, Greenblatt JF, Zhang Z.

TargetScore 1.24.0 – Infer microRNA Targets using microRNA-overexpression data and Sequence Information

TargetScore 1.24.0

:: DESCRIPTION

TargetScore: a probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 TargetScore

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):621-8. doi: 10.1093/bioinformatics/btt599. Epub 2013 Oct 17.
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information.
Li Y1, Goldenberg A, Wong KC, Zhang Z.

spongeScan – Detecting microRNA Binding Elements in lncRNA Sequences

spongeScan

:: DESCRIPTION

spongeScan is a web tool designed to identify and visualize lncRNAs acting as putative miRNA sponges, by searching for multiple miRNA binding sites in lncRNAs.

::DEVELOPER

spongeScan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.
Nucleic Acids Res. 2016 May 19. pii: gkw443.

RNASeqReadSimulator – A Simple RNA-Seq Read Simulator

RNASeqReadSimulator

:: DESCRIPTION

RNASeqReadSimulator is a set of scripts generating simulated RNA-Seq reads. RNASeqReadSimulator provides users a simple tool to generate RNA-Seq reads for research purposes, and a framework to allow experienced users to expand functions.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

  RNASeqReadSimulator

:: MORE INFORMATION

MISO 0.5.4 – RNA-Seq Experiments for Identifying Isoform Regulation

MISO 0.5.4

:: DESCRIPTION

MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MISO

:: MORE INFORMATION

Citation

Yarden Katz, Eric T. Wang, Edoardo M. Airoldi*, Christopher B. Burge*.
Analysis and design of RNA sequencing experiments for identifying isoform regulation
Nature Methods 2010 (7, 1009-1015)

TargetRank 1.0 – Rank Conserved and non-conserved microRNA Targets and siRNA off-targets

TargetRank 1.0

:: DESCRIPTION

 TargetRank is a webtool for ranking conserved and non-conserved microRNA targets and siRNA off-targets.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.G. (2007).
Determinants of targeting by endogeno us and exogenous microRNAs and siRNAs.
RNA 13, 1894-1910.

ExonScan 1.0 – Simulating the RNA Splicing Pattern of a Primary Transcript Sequence

ExonScan 1.0

:: DESCRIPTION

ExonScan expects a primary transcript sequence, preferably excluding the first and last exon. It also currently needs at least about 20 bases upstream of the first exon it can locate, and at least about 60 bases downstream of the last. Numbers in the sequence are discarded, so you can cut and paste from, e.g., a GenBank file.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Cell. 2004 Dec 17;119(6):831-45.
Systematic identification and analysis of exonic splicing silencers.
Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB.

MiRScan 3 – Predict microRNA Genes from pairs of Conserved Sequences

MiRScan 3

:: DESCRIPTION

MiRScan is a computational procedure to identify miRNA genes conserved in more than one genome.

MiRScan Online Version

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Python

:: DOWNLOAD

 MiRScan

:: MORE INFORMATION

Citation

Genome Res. 2007 Dec;17(12):1850-64. Epub 2007 Nov 7.
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.
Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC.

The microRNAs of Caenorhabditis elegans.
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP.
Genes Dev. 2003 Apr 15;17(8):991-1008. Epub 2003 Apr 2.

comRNA 1.80 – Common RNA Secondary Structure Predictor

comRNA 1.80

:: DESCRIPTION

comRNA is a new program that predicts common RNA secondary structure motifs in a group of related sequences.The algorithm applies graph-theoretical approaches to automatically detect common RNA secondary structure motifs in a group of functionally or evolutionarily related RNA sequences.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

comRNA

:: MORE INFORMATION

Citation:

Yongmei Ji, Xing Xu and Gary D. Stormo,
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
, Bioinformatics, 2004 Jul 10; 20(10):1591-1602.”