Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

High-throughput RNAi screening software tools | RNA interference

RNAi is a process in which gene expression is inhibited by small RNA molecules such as small interfering RNAs (siRNAs) and short hairpin RNAs. High-throughput RNAi screening is a breakthrough technology for functional genomics and for drug target…
A A A
HiTSeekR
Web

HiTSeekR High-Throughput Screening Kit for R

A one-stop solution for chemical compound screens, siRNA knock-down and…

A one-stop solution for chemical compound screens, siRNA knock-down and CRISPR/Cas9 knock-out screens, as well as microRNA inhibitor and -mimics screens. HiTSeekR exploits HTS screening data in quite…

A A A
gespeR
Desktop

gespeR Gene-Specific Phenotype EstimatoR

Estimates hidden gene-specific phenotypes (GSPs) from observed reagent-specific…

Estimates hidden gene-specific phenotypes (GSPs) from observed reagent-specific phenotypes (RSPs). gespeR is a statistical model that can be applied to any RNA interference (RNAi) screening data set…

A A A
NSCLC
Desktop

NSCLC Non-Small-Cell Lung Cancer

A computational approach to prioritize candidate drug targets for NSCLC by…

A computational approach to prioritize candidate drug targets for NSCLC by subdividing cell lines into different groups and identifying genetic vulnerabilities targeted to each group. NSCLC uses…

A A A
CARD
Web

CARD Comprehensive Analysis of RNAi Data

Integrates analysis and visualization of RNAi screen data. CARD allows the user…

Integrates analysis and visualization of RNAi screen data. CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target…

A A A
cellHTS
Desktop

cellHTS

A software package implemented in Bioconductor/R to analyze cell-based…

A software package implemented in Bioconductor/R to analyze cell-based high-throughput RNAi screens. The cellHTS2 package is the new version of the cellHTS package, offering improved functionality…

A A A
SAVANAH
Web

SAVANAH

Manages molecular screening libraries across dilution series. SAVANAH aims to…

Manages molecular screening libraries across dilution series. SAVANAH aims to simplify High Throughput Screening (HTS) data management for screening data, supporting both small experiments involving…

A A A
Achilles
Dataset

Achilles

Identifies and catalogues genetic vulnerabilities across hundreds of…

Identifies and catalogues genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. Achilles is a project to facilitates the discovery of context-specific dependencies,…

A A A
HTSvis
Desktop

HTSvis

Provides an R/Shiny open-source web application for interactive visualization…

Provides an R/Shiny open-source web application for interactive visualization and exploratory analysis of arrayed high-throughput data. Using a light-weight infrastructure suitable for desktop…

A A A
HTSanalyzeR
Desktop

HTSanalyzeR

A flexible software to build integrated analysis pipelines for high-throughput…

A flexible software to build integrated analysis pipelines for high-throughput screen (HTS) data that contains over-representation analysis, gene set enrichment analysis, comparative gene set…

A A A
RNAither
Desktop

RNAither

A package for the free statistical environment R which performs an analysis of…

A package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of…

A A A
HTSmix
Desktop

HTSmix

A statistical modeling framework that is based on experimental designs with at…

A statistical modeling framework that is based on experimental designs with at least two controls profiled throughout the experiment, and a normalization and variance estimation procedure with linear…

A A A
displayHTS
Desktop

displayHTS

Provides an analytic tool that can generate figures for displaying data and hit…

Provides an analytic tool that can generate figures for displaying data and hit selection results from HTS experiments. displayHTS can be used to generate not only useful distinctive graphics…

A A A
GUItars
Desktop

GUItars

Enables researchers without a programming background to use strictly…

Enables researchers without a programming background to use strictly standardized mean difference (SSMD) as both a plate quality and a hit selection metric to analyze large data sets. GUItars is…

A A A
SPICE
Web

SPICE shRNA target prediction informed by comprehensive enquiry

A web-based analysis and search tool for investigating biological information…

A web-based analysis and search tool for investigating biological information about shRNA sequences using random oligonucleotides. SPICE displays target candidate genes with sequence alignment as…

A A A
web cellHTS
Web

web cellHTS

A web-based application utility for the end-to-end analysis of large cell-based…

A web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS. The software guides the user through the configuration steps that are required for…

A A A
SIGHTS
Desktop

SIGHTS Statistics and dIagnostic Graphs for HTS

The RVM t-test, available in the SIGHTS software, is a good alternative that…

The RVM t-test, available in the SIGHTS software, is a good alternative that provides all of the advantages of formal statistical testing with as few as two replicates, although a minimum of three is…

A A A
iScreen
Desktop

iScreen image-Based High-content RNAi Screening Analysis Tool

An R package for the statistical modeling and visualization of image-based…

An R package for the statistical modeling and visualization of image-based high-content RNAi screening. The iScreen package provides visualization tools to examine raw data, display analysis results,…

A A A
IQEM
Desktop

IQEM Intensity Quantile Estimation and Mapping

Represents an improvement over existing methods of image non-uniformity (NU)…

Represents an improvement over existing methods of image non-uniformity (NU) correction used in high-content screening (HCS), which are based on varying degrees of simplification to a linear model…

A A A
SbacHTS
Web

SbacHTS Spatial background noise correction for High-Throughput RNAi Screening

A software tool for visualization, estimation and correction of spatial…

A software tool for visualization, estimation and correction of spatial background noise in high-throughput RNAi screens. SbacHTS is supported on the Galaxy open-source framework with a user-friendly…

A A A
HCS-Analyzer
Desktop

HCS-Analyzer

An open source application dedicated to high content screening (HCS)…

An open source application dedicated to high content screening (HCS) multivariate data processing and analysis. HCS-Analyzer includes: (i) a user-friendly interface specifically dedicated to HCS…

A A A
HTS Helper
Desktop

HTS Helper

A handy freeware utility that can be used to process high-throughput screening…

A handy freeware utility that can be used to process high-throughput screening data. The HTS Helper utility has been created to facilitate the systematic error correction of experimental HTS data. It…

A A A
HTS-DB
Dataset

HTS-DB High-Throughput Screening Database

Tracks and stores projects, screens, assays, cell lines and library…

Tracks and stores projects, screens, assays, cell lines and library information. HTS-DB provides full data tracking, interactive data visualization and analysis and comparison of screening results…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.