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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
jmzTab Resource Report Resource Website 1+ mentions |
jmzTab (RRID:SCR_003481) | software resource | A Java interface to the mzTab data exchange format for reporting a summary of proteomics results. | standalone software, mac os x, unix/linux, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24659499 | Apache License, v2 | OMICS_04542, biotools:jmztab | https://bio.tools/jmztab | SCR_003481 | 2026-08-01 12:02:31 | 1 | |||||||
|
metagen Resource Report Resource Website 10+ mentions |
metagen (RRID:SCR_003443) | metagen | software resource | Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17605724 | Free, Available for download, Freely available | OMICS_00238, biotools:metagen | https://www.rdocumentation.org/packages/meta/versions/4.9-6/topics/metagen | SCR_003443 | 2026-08-01 12:02:21 | 18 | ||||||
|
RAREMETAL Resource Report Resource Website 10+ mentions |
RAREMETAL (RRID:SCR_003573) | RAREMETAL | software resource | A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24894501 | biotools:raremetal, OMICS_00243 | https://bio.tools/raremetal | SCR_003573 | 2026-08-01 12:02:15 | 22 | |||||||
|
ShortRead Resource Report Resource Website 100+ mentions |
ShortRead (RRID:SCR_006813) | ShortRead | software resource | Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats. | high throughput sequence data, short read, DNA sequences, short read data |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Bioconductor |
PMID:19654119 | Free, Available for download, Freely available | OMICS_01076 | https://sources.debian.org/src/r-bioc-shortread/ | SCR_006813 | ShortRead - Classes and methods for high-throughput short-read sequencing data. | 2026-08-01 12:03:13 | 225 | |||||
|
EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-08-01 12:03:17 | 19 | |||||
|
RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html, https://bio.tools/ramigo | SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2026-08-01 12:03:19 | 11 | |||||
|
ArtificialFastqGenerator Resource Report Resource Website 10+ mentions |
ArtificialFastqGenerator (RRID:SCR_006880) | ArtificialFastqGenerator | software resource | Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic. | matlab, java, Next Generation Sequencing, aligns reads, reference genome |
is listed by: OMICtools is listed by: Debian |
PMID:23152858 | GNU GPL v3 | OMICS_00248, SCR_015979 | https://sources.debian.org/src/artfastqgenerator/ | SCR_006880 | Artfastqgenerator - Ouputs artificial FASTQ files derived from a reference genome | 2026-08-01 12:03:14 | 10 | |||||
|
BarraCUDA Resource Report Resource Website 1+ mentions |
BarraCUDA (RRID:SCR_006881) | BarraCUDA | software resource | A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: SourceForge |
PMID:22244497 PMID:19451168 |
Acknowledgement requested | OMICS_00650, biotools:barracuda | https://bio.tools/barracuda | SCR_006881 | 2026-08-01 12:03:23 | 4 | ||||||
|
Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna, https://bio.tools/myrna | SCR_006951 | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-08-01 12:03:20 | 2 | |||||
|
FlexProt: flexible protein alignment Resource Report Resource Website 1+ mentions |
FlexProt: flexible protein alignment (RRID:SCR_007306) | software resource | FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
nif-0000-00159, biotools:flexprot | https://bio.tools/flexprot | SCR_007306 | FlexPROT | 2026-08-01 12:03:32 | 1 | ||||||||
|
Taipan Resource Report Resource Website 1+ mentions |
Taipan (RRID:SCR_007330) | Taipan | software resource | A fast hybrid short-read assembly tool. | c, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19535537 | GNU General Public License, v2 | OMICS_00035, biotools:taipan | https://bio.tools/taipan | SCR_007330 | 2026-08-01 12:03:27 | 2 | ||||||
|
ASC Resource Report Resource Website 1+ mentions |
ASC (RRID:SCR_001013) | ASC | software resource | Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. | sample variation, rna, dna, biology, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brown University; Rhode Island; USA |
biotools:sqn, OMICS_01298 | https://bio.tools/sqn | SCR_001013 | 2026-08-01 12:01:36 | 1 | ||||||||
|
jmzML Resource Report Resource Website 1+ mentions |
jmzML (RRID:SCR_001119) | software resource | A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard. | standalone software, mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:20127693 | Free, Available for download, Freely available | biotools:jmzml, OMICS_03340 | https://bio.tools/jmzml | SCR_001119 | 2026-08-01 12:01:23 | 1 | |||||||
|
massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-08-01 12:01:33 | 0 | ||||||
|
Reaper - Demultiplexing trimming and filtering sequencing data Resource Report Resource Website 1+ mentions |
Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) | Reaper | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data. | c, alignment, sequence, demultiplex, trim, filter, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:reaper, OMICS_02157 | https://bio.tools/reaper | SCR_001144 | 2026-08-01 12:01:33 | 1 | |||||||
|
yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-08-01 12:01:27 | 2 | ||||||
|
SplicePlot Resource Report Resource Website |
SplicePlot (RRID:SCR_001172) | SplicePlot | software resource | A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files. | visualization, alternative splicing, splicing quantitative trait loci, quantitative trait loci, rna-seq, hive plot, structure plot, sashmi plot, python, linux, mac os, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University School of Medicine; California; USA |
PMID:24363378 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02185, biotools:spliceplot | https://bio.tools/spliceplot | SCR_001172 | SplicePlot: a tool for visualizing alternative splicing | 2026-08-01 12:01:24 | 0 | |||||
|
les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/, https://bio.tools/les | SCR_001291 | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-08-01 12:01:37 | 0 | ||||||
|
QualiMap Resource Report Resource Website 10+ mentions |
QualiMap (RRID:SCR_001209) | QualiMap | software resource | Software 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. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis. | next-generation sequencing, alignment, linux, macos, windows, quality control, sam, bam, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Economy and Competitiveness BIO2009-10799; EU funded program ERA-NET PathoGenoMics BIO2008-05266-E |
PMID:22914218 DOI:10.1093/bioinformatics/bts503 |
Free, Available for download, Freely available | OMICS_02133, biotools:qualimap | https://bio.tools/qualimap | https://sources.debian.org/src/qualimap/ | SCR_001209 | QualiMap - Evaluating next generation sequencing alignment data | 2026-08-01 12:01:34 | 47 | |||
|
VirusHunter Resource Report Resource Website |
VirusHunter (RRID:SCR_001198) | VirusHunter | software resource | A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses. | virus, next-generation sequencing, roche, 454, taxonomic classification, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:24167629 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:virushunter, OMICS_02153 | https://bio.tools/virushunter | SCR_001198 | 2026-08-01 12:01:34 | 0 |
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