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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Genome Trax Resource Report Resource Website 1+ mentions |
Genome Trax (RRID:SCR_001234) | Genome Trax | service resource | Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia. | next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, database, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: BIOBASE Corporation |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02109, biotools:genome_trax | https://bio.tools/genome_trax | SCR_001234 | SciCrunch Registry | Genome Trax for Next Generation Sequencing | 2026-10-17 01:25:03 | 2 | ||||||
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ChIPMunk Resource Report Resource Website 1+ mentions |
ChIPMunk (RRID:SCR_001191) | ChIPMunk | software resource | DNA motif discovery software adapted for ChIP-Seq data. It is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. It does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences | chip-seq, java, binding, motif, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Russian Federal Agency for Science and Innovation State Contract 02.531.11.9003; Russian Federal Agency for Science and Innovation State Contract 02.740.11.5008; Russian Fund for Basic Research Project 10-04-92663 |
PMID:20736340 | Free, Available for download, Freely available | biotools:chipmunk, OMICS_02140 | https://bio.tools/chipmunk | SCR_001191 | SciCrunch Registry | 2026-10-17 01:25:02 | 2 | |||||
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QUAST Resource Report Resource Website 1000+ mentions |
QUAST (RRID:SCR_001228) | QUAST | software resource | Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots. | genome assembly, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia has parent organization: SourceForge |
PMID:23422339 | biotools:quast, OMICS_02115 | https://bio.tools/quast, https://sources.debian.org/src/quast/ | SCR_001228 | SciCrunch Registry | QUAST: Quality Assessment Tool for Genome Assemblies | 2026-10-17 01:25:03 | 3293 | ||||||
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TileQC Resource Report Resource Website |
TileQC (RRID:SCR_001229) | TileQC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh). | next-generation sequencing, quality control, solexa, r, tile, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Oregon State University; Oregon; USA |
PMID:18507856 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tileqc, OMICS_02114 | https://bio.tools/tileqc | SCR_001229 | SciCrunch Registry | TileQC: A tile based approached to quality control | 2026-10-17 01:24:50 | 0 | |||||
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VAAL Resource Report Resource Website |
VAAL (RRID:SCR_001184) | VAAL | software resource | A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only. | dna sequence, polymorphism, parallel sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:19079253 | biotools:vaal, OMICS_02170 | https://bio.tools/vaal | SCR_001184 | SciCrunch Registry | 2026-10-17 01:24:54 | 0 | |||||||
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Bionimbus Resource Report Resource Website 1+ mentions |
Bionimbus (RRID:SCR_001189) | Bionimbus | service resource | A cloud-based infrastructure for managing, analyzing and sharing genomics datasets. | data sharing, cloud, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Open Science Data Cloud |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:bionimbus, OMICS_02160 | https://bio.tools/bionimbus | SCR_001189 | SciCrunch Registry | 2026-10-17 01:24:54 | 2 | |||||||
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SABER Resource Report Resource Website 50+ mentions |
SABER (RRID:SCR_001257) | SABER | software resource | Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels. | r, linux, ancestry, admixed, genetic, population, linkage disequilibrium, 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:16773560 | Free, Available for download, Freely available | biotools:saber, OMICS_02081 | https://bio.tools/saber | SCR_001257 | SciCrunch Registry | 2026-10-17 01:25:04 | 72 | ||||||
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multtest Resource Report Resource Website 10+ mentions |
multtest (RRID:SCR_001255) | multtest | software resource | Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. | differential expression, microarray, multiple comparison, 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:multtest, OMICS_02085 | https://bio.tools/multtest | SCR_001255 | SciCrunch Registry | multtest - Resampling-based multiple hypothesis testing | 2026-10-17 01:24:51 | 37 | ||||||
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BFCounter Resource Report Resource Website 1+ mentions |
BFCounter (RRID:SCR_001248) | BFCounter | software resource | Software program for counting k-mers in DNA sequence data. It identifies all the k-mers that occur more than once in a DNA sequence data set using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements. | c++, k-mer, dna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:21831268 | Free, Available for download, Freely available | biotools:bfcounter, OMICS_02093 | https://bio.tools/bfcounter | http://pritch.bsd.uchicago.edu/bfcounter.html, http://pritchardlab.stanford.edu/bfcounter.html | SCR_001248 | SciCrunch Registry | BF Counter: Memory efficient K-mer counting Software | 2026-10-17 01:24:55 | 5 | ||||
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TALLYMER Resource Report Resource Website 1+ mentions |
TALLYMER (RRID:SCR_001244) | Tallymer | software resource | A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases. | k-mer, counting, sequence, genome annotation, genome, annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Hamburg; Hamburg; Germany |
PMID:18976482 | Free, Freely available | biotools:tallymer, OMICS_02096 | https://bio.tools/tallymer | SCR_001244 | SciCrunch Registry | 2026-10-17 01:24:55 | 7 | ||||||
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quantsmooth Resource Report Resource Website 1+ mentions |
quantsmooth (RRID:SCR_001271) | quantsmooth | software resource | Software package for quantile smoothing and genomic visualization of array data. | copy number variation, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:15572474 | Free, Available for download, Freely available | OMICS_02067, BioTools:quantsmooth, biotools:quantsmooth | https://bio.tools/quantsmooth, https://bio.tools/quantsmooth, https://bio.tools/quantsmooth | SCR_001271 | SciCrunch Registry | 2026-10-17 01:24:51 | 1 | ||||||
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SNPchip Resource Report Resource Website 10+ mentions |
SNPchip (RRID:SCR_001269) | SNPchip | software resource | Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality. | dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:17204461 | Free, Available for download, Freely available | OMICS_02069, biotools:snpchip | https://bio.tools/snpchip | SCR_001269 | SciCrunch Registry | 2026-10-17 01:24:56 | 14 | ||||||
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ADMIXTURE Resource Report Resource Website 1000+ mentions |
ADMIXTURE (RRID:SCR_001263) | ADMIXTURE | software resource | A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ancestry, macos x, linux, admixture, allele, genome, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
PMID:19648217 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:admixture, OMICS_02077 | http://www.genetics.ucla.edu/software/admixture/ | SCR_001263 | SciCrunch Registry | ADMIXTURE: fast ancestry estimation | 2026-10-17 01:24:51 | 2699 | |||||
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pFind Studio: pLink Resource Report Resource Website 10+ mentions |
pFind Studio: pLink (RRID:SCR_000084) | pLink | software resource | Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mass spectrometry, proteomics, pFind Studio, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:22772728 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02404, biotools:pLink-2 | https://github.com/pFindStudio/pLink3/releases | http://pfind.ict.ac.cn/software/pLink/index.html | SCR_000084 | SciCrunch Registry | , pLink, pLink (pFind Studio), pLink2 | 2026-10-17 01:24:32 | 15 | ||||
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GEOquery Resource Report Resource Website 10+ mentions |
GEOquery (RRID:SCR_000146) | GEOquery | software resource | Software that establishes a bridge between GEO and BioConductor. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: GEO2R has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:17496320 | Free, Available for download, Freely available | biotools:geoquery, OMICS_01972 | https://bio.tools/geoquery, https://sources.debian.org/src/r-bioc-geoquery/ | SCR_000146 | SciCrunch Registry | GEOquery - Get data from NCBI Gene Expression Omnibus (GEO) | 2026-10-17 01:24:36 | 20 | |||||
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GUARDD Resource Report Resource Website |
GUARDD (RRID:SCR_000040) | software resource | MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data. | standalone software, matlab, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:22160811 | Free, Available for download, Freely available | biotools:guardd, OMICS_04020 | https://bio.tools/guardd | SCR_000040 | SciCrunch Registry | Graphical User-friendly Analysis of Relaxation Dispersion Data | 2026-10-17 01:24:31 | 0 | ||||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, data processing software, software application, software resource | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
ADVANCE Program at Brown University ; Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | SciCrunch Registry | Geometric Analysis of Structural Variants | 2026-10-17 01:24:31 | 4 | ||||
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FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | SciCrunch Registry | Fast and Accurate Classification of Sequences | 2026-10-17 01:24:31 | 6 | |||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | consortium, data or information resource, organization portal, portal | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | SciCrunch Registry | 2026-10-17 01:24:37 | 3 | |||||||
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RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software application, software resource | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | SciCrunch Registry | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-10-17 01:24:38 | 115 |
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