Web Apps Other Apps in Development Docker Images Suggestions / Report Issue GitHub

We are a group of researchers applying computational approaches involving the analysis of high-throughput genomic and transcriptomic data aiming to understand how changes at the RNA-level increase proneness to diseases, namely cancer, neurodegenerative disorders and other ageing-related pathologies. Along the way, we develop some tools for assisting non-computational scientists in their analyses of transcriptomic data.

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Our Mission

We develop applications for assisting non-computational scientists in their analyses of transcriptomic data. We aim to contribute towards bridging the conceptual and knowledge gaps between wet- and dry-lab researchers, by transparently sharing our approaches to data analysis in ways that make them understandable and therefore open for scrutiny by fellow scientists, also facilitating their reproducibility. Our bioinformatics tools empower colleagues to intelligibly perform similar analyses to ours, by visually assisting their decision-making process, avoiding “black boxes”. We make our applications open source, user-friendly and freely available on our webserver, to democratise their use by the entire scientific community. We further increase their usability through the creation of accompanying tutorials and other training materials.

Bioinformatic Web Apps

psichomics

Paper [1] [2] R package GitHub

Alternative splicing quantification, visualisation and analysis

Impact (examples): Neurobiology Splicing Regulation Cancer

scStudio

Interactive and flexible analysis of single-cell RNA-seq data

cTRAP

R package GitHub

Identifying candidate causal perturbations from differential gene expression data

Impact (examples):
Cancer

voyAGEr

Paper GitHub Tutorial

Analysis of age-related gene expression changes in human transcriptomic data

betAS

Paper GitHub Tutorial [1] [2]

Intuitive differential alternative splicing analyses using beta distributions

Impact (examples):
Alternative Splicing [1] [2]

Other Apps in Development

CREOLE

GitHub

Reference-free identification of open reading frames and encoded proteins from nanopore transcriptomic long reads

Docker Images

At iMM, we have the opportunity of using Lobo, a multi-hundred node computer cluster. Lobo makes extensive use of Docker images, each a read-only templates that carries the instructions to build a Docker container. Containers are packaged applications that carry the necessary dependencies to allow running the program in every computer environment. The following Docker images were developed by people in the Disease Transcriptomics team (in green, those under active maintenance).

nunoagostinho/

psichomics

alternative-splicing

nunoagostinho/

cTRAP

gene-expression | connectivity-map

nunoagostinho/

bwa

aligner

nunoagostinho/

whippet

alternative-splicing

nunoagostinho/

miso

alternative-splicing

nunoagostinho/

suppa

alternative-splicing

nunoagostinho/

rmats4

alternative_splicing

nunoagostinho/

rmats

alternative_splicing

nunoagostinho/

vast-tools

alternative-splicing

nunoagostinho/

ciri-as

alternative-splicing | circular-RNA

nunoagostinho/

big_matrix_corr

correlation | matrix | big-data

nunoagostinho/

gdc-client

GDC | data-transfer

nunoagostinho/

sailfish

isoform-quantification

nunoagostinho/

parallel-fastq-dump

ncbi | download | fastq

genomeptimm/

fastqc

quality-control | RNA-seq

nunoagostinho/

multiqc

quality-control | RNA-seq

nunoagostinho/

r-machine-learning

R | programming | machine-learning

genomeptimm/

cellranger

scRNA-seq | 10XGenomics

nunoagostinho/

tophat

splice-read | mapper

nunoagostinho/

rsem

transcript-quantification