Software
The following bioinformatics software tools are developed, maintained, or hosted by ELIXIR Ireland associated researchers:
| Tool | Description |
|---|---|
| RiboGalaxy |
An instant of Galaxy tailored for ribosome profiling
data analysis. PMID:
26821742,37356899; DOI:
10.1080/15476286.2016.1141862,10.1016/j.jmb.2023.168043.
Maintainer: Pavel Baranov |
| Trips-viz |
A computational environment for the analysis and
visualisation of public and user-generated ribosome
profiling data mapped to transcriptomes. A component
of
https://riboseq.org. PMID:
30239879,
33950201
; DOI:
10.1093/nar/gky842,
10.1093/nar/gkab323.
Maintainer: Pavel Baranov |
| BRCA-Core |
Source code (Python) to identify protein complexes
co-regulated in tumour proteomic samples.
PMID:29032073
???; DOI:10.1016/j.cels.2017.09.011.
Maintainer: Colm Ryan |
| Homo (v2.1) |
Source code (C++). A program for analysing
compositional heterogeneity across aligned sequences
of nucleotides, genotypes, di-nucleotides, codons or
amino acids (controls the family-wise error rate and
the false discovery rate). The software also computes
three compositional distances and the
p distance (pending publication).
Maintainer: Lars Jermiin |
| SatuRation (v1.0) |
Source code (C++). A program designed to estimate the
degree of saturation observed between two sequences of
nucleotides, genotypes, di-nucleotides, codons or
amino acids (pending publication).
Maintainer: Lars Jermiin |
| AliStat (1.14) |
Source code (C++). Software for quantifying the
completeness of multiple sequence alignments used in
phylogenetic and phylogenomic research. PMID:33575581
; DOI:10.1093/nargab/lqaa024.
Maintainers: Thomas Wong , Lars Jermiin |
| HAL-HAS (v2.6.4) |
Source code (C++). Software for identifying optimal
models of sequences evolution, which uses mixture
models nucleotide sequence evolution that account for
rate heterogeneity across sites and across lineages.
PMID:24927722
; DOI:10.1093/sysbio/syu036
.
Maintainer: Thomas Wong , Lars Jermiin |
| Hetero2 (v2.4) |
Source code (C++). Software to simulate the evolution
of nucleotide sequences on phylogenetic trees under
heterogeneous Markovian conditions. PMID:24927722
; DOI:10.1093/sysbio/syu036
.
Maintainers: Thomas Wong , Lars Jermiin |
| AliJack (v1.0) |
Source code (C++). Software to randomly sample subsets
of sequences from a multiple sequence alignment. The
jackknife procedure is used. PMID:28350004
; DOI:10.1038/srep45302.
Maintainer: Thomas Wong , Lars Jermiin |
| CheckJack (v1.0) |
Source code (C++). Software to compute jackknife
scores from trees generated from alignments generated
using AliJack. PMID:28350004
; DOI:10.1038/srep45302.
Maintainer: Thomas Wong , Lars Jermiin |
| ModelFinder (v1.0) |
Source code (C++). Software for model selection during
phylogenetic analysis of nucleotide and amino acid
sequences. ModelFinder is embedded in IQ-TREE and
IQ-TREE2 and can only be access by downloading these
programs. PMID:28481363
; DOI:10.1038/nmeth.4285.
Maintainers: Minh Bui , Thomas Wong , Lars Jermiin |
| NMF |
An R package for non-negative matrix factorization
Maintainer:Renaud Gaujoux , Cathal Seoighe |
| MREMA |
An R package implementing a mixture of random-effect
meta-analysis. PMID:36197939
; DOI:10.1371/journal.pcbi.1010278.
Maintainer:Dónal O’Shea , Cathal Seoighe |
| PGS-LMM |
Scripts intended to facilitate the calculation of the
LOCO PGS and its inclusion as a fixed effect in a
Linear Mixed Model (LMM) implemented with fastGWA.
PMID:34599249
; DOI:10.1038/s41598-021-99031-3.
Maintainer:Declan Bennett , Cathal Seoighe |
| SLiMs |
Prediction of function and 2D structures for proteins,
protein motifs and peptides (see
BioWare
or
DistillDeep).
Maintainer:Gianluca Pollastri , Denis Shields |
| autopeptideML |
AutoPeptideML is a tool that automates the development
of ML models for predicting peptide bioactivity,
facilitating robust evaluation and reproducibility.
PMID:
39292535; DOI:
10.1093/bioinformatics/btae555.
Maintainer: Raul Fernandez-Diaz |
| Clustal Omega |
Multiple Sequence Alignment package via on-line
server, in collaboration with groups in Germany, the
UK and France. PMID:21988835
; DOI:10.1038/msb.2011.75.
Maintainer: |
| demuxSNP |
R/Bioconductor package that assists in demultiplexing
scRNAseq data using both cell hashing and SNPs data.
Maintainer: Michael Lynch , Aedin Culhane |
| corral |
R/Bioconductor package for correspondence analysis for
single-cell data.
Maintainer: Lauren Hsu , Aedin Culhane |
| SingleCellMultiModal |
R/Bioconductor package providing multimodal
single-cell RNA-seq datasets for benchmarking and
method development.
Maintainer: Marcel Ramos , Aedin Culhane |
| mogsa |
R/Bioconductor package for multi-omics gene set
analysis.
Maintainer: Chen Meng , Aedin Culhane |
| iBBiG |
R/Bioconductor package for iterative binary
bi-clustering that extracts groups of phenotypes from
multiple studies that are associated with similar gene
sets.
Maintainer: Aedin Culhane |
| made4 |
R/Bioconductor package for multivariate analysis of
microarray data.
Maintainer: Aedin Culhane |