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

Experimental design software tools | RNA sequencing data analysis

RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and…
G T A T C G C T A
SSA
Web
Desktop

SSA Submodular Selection of Assays

Chooses a diverse panel of genomic assays that leverages methods from…

Chooses a diverse panel of genomic assays that leverages methods from submodular optimization. SSA serves as a model for how submodular optimization can be applied to other discrete problems in…

G T A T C G C T A
AnalyzeReplicat…
Desktop

AnalyzeReplication

A cost-effectiveness metric for guiding the design of large-scale RNA-seq…

A cost-effectiveness metric for guiding the design of large-scale RNA-seq Differential Expression (DE) studies. AnalyzeReplication is able to improve a single target: power to detect DE genes between…

G T A T C G C T A
rnaseqmixture
Dataset

rnaseqmixture

A RNA-sequencing data set. rnaseqmixture provides a valuable resource for…

A RNA-sequencing data set. rnaseqmixture provides a valuable resource for benchmarking different protocols and data pre-processing workflows. The classic mixture design allows precision and bias to…

G T A T C G C T A
powsimR
Desktop

powsimR

Simulates and evaluates differential expression from bulk and especially…

Simulates and evaluates differential expression from bulk and especially single-cell RNA-seq data. powsimR can not only estimate sample sizes necessary to achieve a certain power, but also informs…

G T A T C G C T A
casper
Desktop

casper

Infer alternative splicing from paired-end RNA-seq data. The model is based on…

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start…

G T A T C G C T A
ssizeRNA
Desktop

ssizeRNA Sample Size Calculation for RNA-Seq Experimental Design

Implements a procedure for sample size calculation while controlling false…

Implements a procedure for sample size calculation while controlling false discovery rate (FDR) for RNA-sequencing experimental design. ssizeRNA procedure is based on the weighted linear model…

G T A T C G C T A
Scotty
Web

Scotty

A tool to assist in the designing of RNA Seq experiments that have adequate…

A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.

G T A T C G C T A
samExploreR
Desktop

samExploreR

An R package that allows the subsampling (m out of n bootstraping) of…

An R package that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design.…

G T A T C G C T A
BwB
Desktop

BwB BioDepot-workflow-Builder

Aims to provide a user-friendly, modular and open-source graphical user…

Aims to provide a user-friendly, modular and open-source graphical user interface (GUI) to create bioinformatics workflows. BioDepot-workflow-Builder (BwB) is a portable and open-source tool for…

G T A T C G C T A
PROPER
Desktop

PROPER PROspective Power Evaluation for RNAseq

An R package for power assessment and sample size determination for RNA-seq.…

An R package for power assessment and sample size determination for RNA-seq. PROPER includes two components: (i) a semi-parametric simulation that generates data based on actual RNA-seq experiments…

G T A T C G C T A
A sample size…
Desktop

A sample size calculation method

Sample size calculation based on exact test for assessing differential…

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author.

G T A T C G C T A
RNAtor
Mobile

RNAtor

Aids biologists in correctly designing their RNA-seq experiments. RNAtor is a…

Aids biologists in correctly designing their RNA-seq experiments. RNAtor is a mobile application for Android platforms a biologist-friendly and easy-to-use platform to design RNA-seq experiments…

G T A T C G C T A
subSeq
Desktop

subSeq

Performs subsampling sequencing reads with binomial sampling. After…

Performs subsampling sequencing reads with binomial sampling. After constructing subsamples and performing an analysis on each, subSeq calculates and visualizes summary metrics about each sequencing…

G T A T C G C T A
RNASeqPower
Desktop

RNASeqPower

Helps investigators optimally design RNA-Seq experiments. RNASeqPower can…

Helps investigators optimally design RNA-Seq experiments. RNASeqPower can predict the effect of adding more sequencing depth or biological replicates on calling differential expressed genes. It also…

G T A T C G C T A
RNASeqPowerCalc…
Desktop

RNASeqPowerCalculator

A power analysis tool that captures the dispersion in the data and can serve as…

A power analysis tool that captures the dispersion in the data and can serve as a practical reference under the budget constraint of RNA-Seq experiments.

G T A T C G C T A
RSPS
Desktop

RSPS RNA-Seq Power Simulation

Uses an efficient simulation algorithm to empirically determine statistical…

Uses an efficient simulation algorithm to empirically determine statistical power and necessary sample size for RNA-Seq studies. RSPS simulates the data from Poisson (no overdispersion) or Negative…

G T A T C G C T A
RnaSeqSampleSiz…
Web
Desktop

RnaSeqSampleSize

Provides a sample size estimation method based on the distributions of gene…

Provides a sample size estimation method based on the distributions of gene read counts and dispersions from real data. RnaSeqSampleSize uses datasets from the user’s preliminary experiments or The…

G T A T C G C T A
RNAseqPS
Web

RNAseqPS

An advanced online RNAseq power and sample size calculation tool based on the…

An advanced online RNAseq power and sample size calculation tool based on the Poisson and negative binomial distributions. RNAseqPS was built using the Shiny package in R. It provides an interactive…

Information

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