Repositories list

• IsoAnnot

  Public
  Python

  •1•6•1•0•Updated Sep 20, 2025Sep 20, 2025

• SQANTI3

  Public
  Tool for the Quality Control of Long-Read Defined Transcriptomes

  HTML

  •

  GNU General Public License v3.0

  •57•238•12•0•Updated Sep 17, 2025Sep 17, 2025

• TensorPLS

  Public
  R

  •0•0•0•0•Updated Sep 16, 2025Sep 16, 2025

• SQANTI-SIM

  Public
  A simulator of controlled transcript novelty for lrRNA-seq benchmark

  HTML

  •

  GNU General Public License v3.0

  •2•9•1•0•Updated Sep 11, 2025Sep 11, 2025

• green-computing

  Public
  Repository for green computing resources to be shared and improved,

  0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• tappAS

  Public
  This repository contains the source code for the tappAS application. See README for details.

  Java

  •4•19•16•0•Updated Jul 29, 2025Jul 29, 2025

• RColorConesa

  Public
  Conesa Palette for R

  R

  •

  Other

  •0•6•0•0•Updated Jun 27, 2025Jun 27, 2025

• courses-SQANTI_verse

  Public
  HTML

  •0•3•0•0•Updated Jun 25, 2025Jun 25, 2025

• paintomics4

  Public
  JavaScript

  •

  GNU General Public License v3.0

  •0•8•0•0•Updated Apr 23, 2025Apr 23, 2025

• MOSim

  Public
  Bulk and single-cell Multi-Omics ground truth Simulator in R

  R

  •1•10•2•0•Updated Apr 2, 2025Apr 2, 2025

• Github-stats-saver

  Public
  Scripts to store downloads or otherwise relevant metrics of a program from different repositories

  Python

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Feb 17, 2025Feb 17, 2025

• SQANTI_reads_ComputationalEfficiency_plots

  Public
  Storage of scripts to reproduce the computational efficiency evaluation in Keil, Monzó, McIntyre, Conesa. 2025. SQANTI-reads

  Shell

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• MultiPower

  Public
  Statistical power studies for multi-omics experiments.

  R

  •10•32•3•0•Updated Jan 18, 2025Jan 18, 2025

• beanTFBSs

  Public
  Python

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• Coxmos

  Public
  Survival Analyses for High Dimensional Data

  HTML

  •

  Creative Commons Attribution 4.0 International

  •0•2•0•0•Updated Mar 10, 2024Mar 10, 2024

• MORE

  Public
  Discover regulatory relationships for multi-omics data using regression models.

  R

  •1•5•0•0•Updated Mar 5, 2024Mar 5, 2024

• acorde

  Public
  Isoform co-usage networks from single-cell RNA-seq data

  HTML

  •

  GNU General Public License v3.0

  •6•16•0•0•Updated Feb 21, 2024Feb 21, 2024

• SQANTI

  Public
  Python

  •

  MIT License

  •3•13•0•0•Updated Apr 26, 2023Apr 26, 2023

• MAMBA

  Public
  MATLAB

  •

  GNU General Public License v2.0

  •0•2•0•0•Updated Oct 11, 2022Oct 11, 2022

• TCR_nextflow

  Public
  Nextflow

  •2•12•1•0•Updated Feb 17, 2022Feb 17, 2022

• MultiBaC

  Public
  Single and multiomic batch effect correction

  R

  •2•7•5•0•Updated Jan 21, 2022Jan 21, 2022

• Perspective_Multi-Omics_Integration

  Public
  Repository containing supplementary code for Tarazona et al. 2021, Nat. Comp. Sci.

  HTML

  •0•0•0•0•Updated May 13, 2021May 13, 2021

• NOISeq

  Public
  NOISeq package

  0•2•2•0•Updated May 4, 2021May 4, 2021

• Padhoc

  Public
  Text mining tool for biological pathways reconstruction

  Python

  •0•6•0•0•Updated Apr 15, 2021Apr 15, 2021

• TEDDY_Multi-Omics_Integration

  Public
  R

  •1•1•1•0•Updated Jan 14, 2021Jan 14, 2021

• MirCure

  Public
  microRNA quality control, filter, and curation.

  R

  •

  GNU General Public License v3.0

  •0•5•0•0•Updated Jan 5, 2021Jan 5, 2021

• DeCovid

  Public
  Transcriptomics analysis for COVID-19 Disease Map genes.

  R

  •0•0•0•0•Updated Dec 10, 2020Dec 10, 2020

• MHE_Multi-Omics_Integration

  Public
  MHE: Mimimal Hepatic Encephalopathy

  R

  •0•0•0•0•Updated Nov 6, 2020Nov 6, 2020

• MDM

  Public
  Workflow and package for network approach to study the role of microbial dark matter (MDM)

  R

  •

  Other

  •5•6•1•0•Updated Jul 31, 2020Jul 31, 2020

• MultiMip6

  Public
  0•1•0•0•Updated Jan 31, 2020Jan 31, 2020