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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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QCGWAS Resource Report Resource Website 1+ mentions |
QCGWAS (RRID:SCR_006408) | QCGWAS | software resource | Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies. | quality control, genome wide association study, windows, os x, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24395754 | GNU General Public License, v3 or later | OMICS_02203, biotools:qcgwas | https://bio.tools/qcgwas | SCR_006408 | QCGWAS: Quality Control of Genome Wide Association Study results, Quality Control of Genome Wide Association Study | 2026-07-25 12:06:19 | 7 | |||||
|
ROMPREV Resource Report Resource Website |
ROMPREV (RRID:SCR_009361) | ROMPREV | software application, software resource | Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, any with r installation, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154577, biotools:romprev | https://bio.tools/romprev | SCR_009361 | Regression of Offspring on Mid-Parent (REVised) | 2026-07-26 09:04:49 | 0 | |||||||
|
SIMULATE Resource Report Resource Website 10+ mentions |
SIMULATE (RRID:SCR_009391) | software application, software resource | Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-dos, vms, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154630, biotools:simulate | https://bio.tools/simulate | SCR_009391 | 2026-07-26 09:05:01 | 11 | |||||||||
|
MaCH-Admix Resource Report Resource Website 10+ mentions |
MaCH-Admix (RRID:SCR_009598) | software application, software resource | A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix. | genomic analysis, imaging genomics, imputation, snp, gene, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23074066 | Free, Non-commercial, Acknowledgement requested | nlx_155800, biotools:mach-admix | http://www.nitrc.org/projects/mach-admix, https://bio.tools/mach-admix | SCR_009598 | MaCH-Admix: Genotype Imputation Software | 2026-07-26 09:04:54 | 18 | ||||||
|
ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar, https://bio.tools/annovar | SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-07-26 09:05:48 | 5946 | |||||
|
SASQUANT Resource Report Resource Website 1+ mentions |
SASQUANT (RRID:SCR_013122) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154610, biotools:sasquant | https://bio.tools/sasquant | SCR_013122 | 2026-07-26 09:05:50 | 4 | ||||||||
|
QMSIM Resource Report Resource Website 50+ mentions |
QMSIM (RRID:SCR_013123) | software application, software resource | Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154560, biotools:qmsim | https://bio.tools/qmsim | SCR_013123 | Qtl and Marker SIMulator | 2026-07-26 09:05:50 | 57 | ||||||||
|
MendelIHT.jl Resource Report Resource Website 1+ mentions |
MendelIHT.jl (RRID:SCR_018292) | software application, software resource | Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs. | GWAS, iterative hard thresholding, multiple regression, GLM model, feature selection, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PLINK |
DOI:10.1101/697755 | Free, Available for download, Freely available | biotools:mendeliht.jl | https://bio.tools/mendeliht.jl | SCR_018292 | Mendel Iterative Hard Thresholding.jl, Mendel Iterative Hard Thresholding, MendelIHT | 2026-07-26 09:07:13 | 2 | ||||||
|
BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software application, software resource | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; German Research Foundation ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | Bioconda | 2026-07-26 09:07:14 | 66 | |||||
|
CorrDrugTumorMSI Resource Report Resource Website 1+ mentions |
CorrDrugTumorMSI (RRID:SCR_018962) | software application, software resource | Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data. | Drug, tumor heterogeneity, mass spectrometry imaging, spatial methods, drug distribution correlation, tumor tissue types, MSI, imaging data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:corrdrugtumormsi | https://bio.tools/corrdrugtumormsi | SCR_018962 | 2026-07-26 09:07:18 | 1 | ||||||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-07-26 09:07:10 | 5 | |||||
|
BioBERT Resource Report Resource Website 10+ mentions |
BioBERT (RRID:SCR_017547) | software application, software resource | Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. | Pretrained, biomedical, language, representation, model, text, mining, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BERT |
National Research Foundation of Korea | DOI:10.1093/bioinformatics/btz682 | Free, Available for download, Freely available | biotools:biobERt | https://github.com/naver/biobert-pretrained, https://bio.tools/BioBERT | SCR_017547 | Bidirectional Encoder Representations from Transformers for Biomedical Text Mining | 2026-07-26 09:07:06 | 45 | |||||
|
GeCo3 Resource Report Resource Website 1+ mentions |
GeCo3 (RRID:SCR_018877) | software application, software resource | Software tool as DNA compressor that uses neural network to do mixing of experts. | DNA compressor, neural network, expert mixing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:geco3 | https://bio.tools/geco3 | SCR_018877 | 2026-07-26 09:07:23 | 2 | ||||||||
|
BayesEpiModels Resource Report Resource Website 1+ mentions |
BayesEpiModels (RRID:SCR_019291) | software application, software resource | Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework. | Stochastic growth model, Stochastic SIR model, Bayesian inference, epidemiological models, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:bayesepimodels | https://bio.tools/bayesepimodels | SCR_019291 | 2026-07-26 09:07:23 | 1 | ||||||||
|
PEPPER Resource Report Resource Website 1+ mentions |
PEPPER (RRID:SCR_000431) | PEPPER | software application, software resource | A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...). | plugin, protein-protein interaction, network, bio.tools |
is listed by: OMICtools is listed by: Cytoscape is listed by: bio.tools is listed by: Debian |
PMID:25138169 | Free, Available for download, Freely available | biotools:pepper, OMICS_05485 | https://bio.tools/pepper | SCR_000431 | Protein complex Expansion using Protein-Protein intERaction networks, Protein complex Expansion using Protein-Protein intERactions | 2026-07-26 09:02:47 | 1 | |||||
|
GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-07-26 09:03:05 | 451 | |||||
|
BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-07-26 09:03:04 | 370 | ||||||
|
HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software application, software resource | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-07-26 09:03:03 | 45 | |||||
|
PEDHUNTER Resource Report Resource Website 1+ mentions |
PEDHUNTER (RRID:SCR_002031) | PedHunter | software application, software resource | Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot. | gene, genetic, genomic, genealogy, pedigree, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
PMID:20433770 PMID:9521925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pedhunter, OMICS_00211, nlx_154518 | https://bio.tools/pedhunter | SCR_002031 | 2026-07-26 09:03:08 | 2 | ||||||
|
cortex Resource Report Resource Website 100+ mentions |
cortex (RRID:SCR_002467) | cortex | software application, software resource | Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clinical neuroinformatics, mgh/mgz, magnetic resonance, r, surface analysis, thickness, mri, cortical thickness, morphometry, neuroimaging, power analysis, study design, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: bio.tools is listed by: Debian has parent organization: Brain Research Institute |
PMID:22807270 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155842, biotools:cortex | http://brain.org.au/software/cortex/power, http://www.nitrc.org/projects/cortex, https://bio.tools/cortex | SCR_002467 | Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies | 2026-07-26 09:03:14 | 374 |
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