Genomics of Gene Expression

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

For multiomics experiments: estimate the sample size needed to achieve a given statistical power per omic and globally.

multiml

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
Application with a Graphical Inteface and a command-line interface to facilitate the quality control of alignment sequencing data.

Storage

stategra

EMS designed for storage and annotation of complex NGS and omics experiments (proteomics and metabolomics).

Statistical Analysis

more

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

Non-parametric approach for the identification of differentially expressed genes from count data.

masigpro

Identify genes that show different gene expression profiles across analytical groups in time-course experiments.

plsplm

asca genes

Method for the multivariate analysis of multifactorial gene expression datasets

masigfun

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.