SbacHTS v5 – Spatial background correction for High-Throughput RNAi Screening

SbacHTS v5

:: DESCRIPTION

SbacHTS is a software for visualization, estimation and correction of spatial background noises of RNAi screening experiment results.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 SbacHTS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2218-20. doi: 10.1093/bioinformatics/btt358. Epub 2013 Jun 28.
SbacHTS: spatial background noise correction for high-throughput RNAi screening.
Zhong R1, Kim MS, White MA, Xie Y, Xiao G.

OfftargetFinder – web tool for species-specific RNAi Design

OfftargetFinder

:: DESCRIPTION

OfftargetFinder is a web tool for species-specific RNAi design.

::DEVELOPER

OfftargetFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 OfftargetFinder

:: MORE INFORMATION

Citation:

OfftargetFinder: a web tool for species-specific RNAi design.
Good RT, Varghese T, Golz JF, Russell DA, Papanicolaou A, Edwards O, Robin C.
Bioinformatics. 2015 Dec 24. pii: btv747.

SI-FI 3.2 – RNAi (RNA interference) Off-target Prediction

SI-FI 3.2

:: DESCRIPTION

si-Fi (siRNA Finder) is a Software for RNAi (RNA interference) off-target prediction.The software is designed for checking long-double stranded RNAi constructs for target specificity and silencing efficiency. It can be used also to select sequence regions suitable for designing RNAi constructs. The program provides clear tabular and graphical outputs.

::DEVELOPER

Stefanie Lück

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SI-FI

:: MORE INFORMATION

RNAinteract 1.18.0 / RNAinteractMAPK 1.8.0 – Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi

RNAinteract 1.18.0 / RNAinteractMAPK 1.8.0

:: DESCRIPTION

RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images.

RNAinteractMAPK is a software of Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi

::DEVELOPER

Bernd Fischer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  RNAinteract  / RNAinteractMAPK 

:: MORE INFORMATION

Citation

Thomas Horn, Thomas Sandmann, Bernd Fischer, Elin Axelsson, Wolfgang Huber, Michael Boutros,
Mapping of signaling networks through synthetic genetic interaction analysis by RNAi,
Nature methods 8 (4), 341-346, 2011.

cellHTS2 2.35.0 / web cellHTS2 – Analysis of Cell-based RNAi Screens

cellHTS2 2.35.0 / web cellHTS2

:: DESCRIPTION

cellHTS2 is a software package implemented in Bioconductor/R to analyze cell-based high-throughput RNAi screens.

web cellHTS provides a user-friendly interface to cellHTS and a step-by-step tutorial how to use cellHTS for the analysis of high-throughput screening experiments.

::DEVELOPER

Boutros group & Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor
  • Java

:: DOWNLOAD

  cellHTS2 / web cellHTS2

:: MORE INFORMATION

Citation

Genome Biol. 2006;7(7):R66.
Analysis of cell-based RNAi screens.
Boutros M, Brás LP, Huber W.

Pelz., O., Gilsdorf, M., Boutros, M. (2010).
web cellHTS2: A web application for the analysis of high-throughput screening data.
BMC Bioinformatics 11:185.

RNAither 2.18.0 – Statistical analysis of high-throughput RNAi screens

RNAither 2.18.0

:: DESCRIPTION

RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.

::DEVELOPER

Lars Kaderali <lars.kaderali at tu-dresden.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 RNAither

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):678-9. doi: 10.1093/bioinformatics/btp014. Epub 2009 Jan 25.
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.
Rieber N1, Knapp B, Eils R, Kaderali L.

dsCheck — Off-target Search website for dsRNA-mediated RNAi

dsCheck

:: DESCRIPTION

dsCheck is a web-based online software for estimating off-target effects caused by the long double-stranded RNA (dsRNA) used in RNAi studies.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W589-91.
dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.
Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita S.

iScreen 1.0 – Image-Based High-content RNAi Screening Analysis Tool

iScreen 1.0

:: DESCRIPTION

iScreen is an R package for the statistical modeling and visualization of image-based high-content RNAi screening.

::DEVELOPER

Rui Zhong <rui.zhong@utsouthwestern.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • R

:: DOWNLOAD

 iScreen

:: MORE INFORMATION

Citation:

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.
Zhong R, Dong X, Levine B, Xie Y, Xiao G.
J Biomol Screen. 2014 Dec 29. pii: 1087057114564348.

E-RNAi 3.2 – Design Optimized RNAi Constructs

E-RNAi 3.2

:: DESCRIPTION

E-RNAi is a tool for the design and evaluation of RNAi reagents for a variety of species. It can be used to design and evaluate long dsRNAs (including esiRNAs) as well as siRNAs.

::DEVELOPER

E-RNAi team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser 

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E-RNAi: a web application for the multi-species design of RNAi reagents–2010 update.
Thomas Horn; Michael Boutros
Nucl. Acids Res. (2010) 38 (suppl 2): W332-W339. doi: 10.1093/nar/gkq317

NePhe 1.0 – Network RNAi Phenotype Score

NePhe 1.0

:: DESCRIPTION

NePhe (Network RNAi Phenotype) is intended to implement a network-based integrative approach to prioritize reliable hits in genome-wide screens

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NePhe

:: MORE INFORMATION

Citation

Wang L, Tu Z, Sun FZ (2009)
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.
BMC Genomics 10:220.