Long-Reads
sqanti3
SQANTI3 is an automated pipeline for the classification and quality-control evaluation of long-read transcriptomes.
isoannot
IsoAnnotLite: your application for the annotation of transcriptomes.
tappas
tappAS is a Java GUI application for the analysis of RNA-Seq data down to the isoform level.
Experimental Design
multipower
In multi-omic experiments, MultiPower estimates the sample size needed to achieve a given statistical power per omic and globally.
multiml
The MultiML method is designed to help users determine the optimal sample size required to control for classification error rates when using one or more omics datasets.
Quality Control
multibac
R package for the removal of multi-omics batch effects.
arsyn
Multivariate approach to correct batch effects in multifactorial gene expression datasets.
qualimap
Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.
Storage
stategra
The STATegraEMS is an EMS designed for storage and annotation of complex NGS and omics experiments (proteomics and metabolomics data).
Statistical Analysis
more
MORE is a method which facilitate the task of applying GLMs models to multi-omic data. The goal of MORE is to model gene expression as a function of experimental variables.
mamba
A Multiomic integration approach.
acorde
An end-to-end pipeline designed for the study of isoform co-usage networks using single-cell RNA-seq data (scRNA-seq).
noiseq
NOISeq is a non-parametric approach for the identification of differentially expressed genes from count data or previously normalized count data.
masigpro
maSigPro is a statistical procedure to identify genes that show different gene expression profiles across analytical groups in time-course experiments.
masigfun
asca genes
Method for the multivariate analysis of multifactorial gene expression datasets
plsplm
Visualization
blast2go
Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.
padhoc
A computational pipeline for pathway reconstruction on the fly
paintomics
Web tool for the integrative visualization of multiple omic datasets onto KEGG, Reactome, and MapMan pathways.
spongescan
Web tool designed to identify and visualize lncRNAs acting as putative miRNA sponges, by searching for multiple miRNA binding sites in lncRNAs.
rgmatch
RGmatch is a flexible and easy-to-use tool to match genomic regions to the closest gene (also transcript or exon), which provides the area of the gene where the region overlaps.