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.

Tutorial

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 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.