RNAHeliCes 2.0.14 – RNA Folding Space Analysis

RNAHeliCes 2.0.14

:: DESCRIPTION

RNAHeliCes is a tool for RNA folding space analysis. It abstracts from structural detail and maps structures using a position-specific abstraction based on helices.

::DEVELOPER

Cyanolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RNAHeliCes

:: MORE INFORMATION

Citation:

RNA. 2012 Dec;18(12):2135-47. doi: 10.1261/rna.033548.112. Epub 2012 Oct 25.
Abstract folding space analysis based on helices.
Huang J1, Backofen R, Voß B.

iLncRNAdis-FB – Identify potential lncRNA-disease Associations

iLncRNAdis-FB

:: DESCRIPTION

iLncRNAdis-FB is a new predictor for identifying lncRNA-disease associations by fusing biological feature blocks through deep neural network

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wei H, Liao Q, Liu B.
iLncRNAdis-FB: identify lncRNA-disease associations by fusing biological feature blocks through deep neural network.
IEEE/ACM Trans Comput Biol Bioinform. 2020 Jan 6;PP. doi: 10.1109/TCBB.2020.2964221. Epub ahead of print. PMID: 31905146.

iPiDi-PUL – Identifying Piwi-interacting RNA-disease Associations based on Positive Unlabeled Learning

iPiDi-PUL

:: DESCRIPTION

iPiDi-PUL is an inspiring method which identifies novel piRNA-disease associations via positive unlabeled learning.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wei H, Xu Y, Liu B.
iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning.
Brief Bioinform. 2021 May 20;22(3):bbaa058. doi: 10.1093/bib/bbaa058. PMID: 32393982.

iMiRNA-PseDPC – microRNA Precursor Identification with a Pseudo Distance-pair Composition Approach

iMiRNA-PseDPC

:: DESCRIPTION

The web-server iMiRNA-PseDPC was developed for identifying the real microRNA precursors and false microRNA precursors.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2015 Feb 3:1-28. [Epub ahead of print]
iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach.
Liu B1, Fang L, Liu F, Wang X, Chou KC.

repRNA – Web Server for Generating Various Modes of RNA Sequences

repRNA

:: DESCRIPTION

repRNA (representations of RNA sequences) is a web server for generating various modes of RNA sequences

::DEVELOPER

Bin Liu’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Genet Genomics. 2015 Jun 18.
repRNA: a web server for generating various feature vectors of RNA sequences.
Liu B1, Liu F, Fang L, Wang X, Chou KC.

miRNA-deKmer – Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy

miRNA-deKmer

:: DESCRIPTION

miRNA-deKmer is a web server of identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.
Liu B, Fang L, Wang S, Wang X, Li H, Chou KC.
J Theor Biol. 2015 Nov 21;385:153-9. doi: 10.1016/j.jtbi.2015.08.025.

iMcRNA / miRNA-dis – microRNA Precursor Identification based on Distance Structure Status Pairs

 iMcRNA / miRNA-dis

:: DESCRIPTION

The web-server iMcRNA was developed for identifying the real microRNA precursors and false microRNA precursors.

miRNA-dis: microRNA precursor identification based on distance structure status pairs

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Identification of real microRNA precursors with a pseudo structure status composition approach.
Liu B, Fang L, Liu F, Wang X, Chen J, Chou KC.
PLoS One. 2015 Mar 30;10(3):e0121501. doi: 10.1371/journal.pone.0121501.

Mol Biosyst. 2015 Apr;11(4):1194-204. doi: 10.1039/c5mb00050e.
miRNA-dis: microRNA precursor identification based on distance structure status pairs.
Liu B1, Fang L, Chen J, Liu F, Wang X.

PmiREN 2.0 – A comprehensive Encyclopedia of Plant miRNAs

PmiREN 2.0

:: DESCRIPTION

PmiREN (Plant miRNA ENcyclopedia) is a comprehensive functional plant miRNA database.

::DEVELOPER

Yang lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Guo Z, Kuang Z, Wang Y, Zhao Y, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T, Cao X, Wei J, Li L, Yang X.
PmiREN: a comprehensive encyclopedia of plant miRNAs.
Nucleic Acids Res. 2020 Jan 8;48(D1):D1114-D1121. doi: 10.1093/nar/gkz894. PMID: 31602478; PMCID: PMC6943064.

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.

RCAS 1.18.0 – RNA Centric Annotation System

RCAS 1.18.0

:: DESCRIPTION

RCAS facilitates biological discovery from target regions located by methods such as Clip-Seq. RCAS automatically provides dynamic annotations for custom input files that contain transcriptomic target regions.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

RCAS

:: MORE INFORMATION

Citation

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120. PMID: 28334930; PMCID: PMC5449606.