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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LAMARC Resource Report Resource Website 10+ mentions |
LAMARC (RRID:SCR_009252) | LAMARC | software application, software resource | Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1016/j.tree.2008.09.007 | OMICS_28408, nlx_154420 | https://sources.debian.org/src/lamarc/ | SCR_009252 | Likelihood Analysis with Metropolis Algorithm using Random Coalescence | 2026-09-19 12:58:02 | 46 | ||||||
|
HS-TDT Resource Report Resource Website 1+ mentions |
HS-TDT (RRID:SCR_009240) | HS-TDT | software application, software resource | Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154401, biotools:hs-tdt | https://bio.tools/hs-tdt | SCR_009240 | Haplotype Sharing Transmission Disequilibrium Test | 2026-09-19 12:58:02 | 4 | |||||||
|
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) | 2026-09-19 12:58:05 | 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 | 2026-09-19 12:58:06 | 12 | |||||||||
|
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 | 2026-09-19 12:58:07 | 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 | 2026-09-19 12:58:08 | 6463 | |||||
|
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 | 2026-09-19 12:58:09 | 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 | 2026-09-19 12:58:09 | 63 | ||||||||
|
PerlPrimer Resource Report Resource Website 100+ mentions |
PerlPrimer (RRID:SCR_012038) | software application, software resource | A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:15073005 DOI:10.1093/bioinformatics/bth254 |
Open unspecified license | OMICS_02354 | https://sources.debian.org/src/perlprimer/ | SCR_012038 | PerlPrimer - open-source PCR primer design | 2026-09-19 12:58:08 | 247 | |||||||
|
BoolNet Resource Report Resource Website 1+ mentions |
BoolNet (RRID:SCR_024264) | software resource, software toolkit | Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks. | reconstruct, generate, simulate, synchronous, asynchronous, probabilistic, temporal, Boolean networks, | is listed by: Debian | PMID:20378558 | Free, Available for download, Freely available, | OMICS_06963 | https://sources.debian.org/src/r-cran-boolnet/ | SCR_024264 | BoolNet: Construction, Simulation and Analysis of Boolean Networks, r-cran-boolnet | 2026-09-19 12:56:21 | 2 | ||||||
|
cmprsk Resource Report Resource Website 1+ mentions |
cmprsk (RRID:SCR_024265) | software resource, software toolkit | Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks. | estimation, testing, regression modeling, subdistribution functions in competing risks, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-cmprsk/ | SCR_024265 | cmprsk: Subdistribution Analysis of Competing Risks, r-cran-cmprsk | 2026-09-19 12:56:21 | 3 | ||||||||
|
bio3d Resource Report Resource Website 100+ mentions |
bio3d (RRID:SCR_024266) | software resource, software toolkit | Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data. | comparative analysis of protein structures, process protein structure, organize and explore protein structure, sequence and dynamics data, | is listed by: Debian | PMID:16940322 | Free, Available for download, Freely available, | OMICS_12577 | https://sources.debian.org/src/r-cran-bio3d/ | SCR_024266 | r-cran-bio3d, bio3d: Biological Structure Analysis | 2026-09-19 12:56:21 | 341 | ||||||
|
DoseFinding Resource Report Resource Website 1+ mentions |
DoseFinding (RRID:SCR_024268) | software resource, software toolkit | Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology. | dose finding experiments design and analysis functions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dosefinding/ | SCR_024268 | DoseFinding: Planning and Analyzing Dose Finding Experiments, r-cran-dosefinding | 2026-09-19 12:56:21 | 1 | ||||||||
|
distory Resource Report Resource Website |
distory (RRID:SCR_024269) | software resource, software toolkit | Software R package for geodesic distance between phylogenetic trees and associated functions. | geodesic distance, phylogenetic trees, associated functions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33012 | https://sources.debian.org/src/r-cran-distory/ | SCR_024269 | distory: Distance Between Phylogenetic Histories, r-cran-distory | 2026-09-19 12:56:21 | 0 | |||||||
|
alakazam Resource Report Resource Website 1+ mentions |
alakazam (RRID:SCR_024261) | software resource, software toolkit | Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. | high throughput adaptive immune receptor repertoire sequencing analysis, sequencing analysis, | is listed by: Debian | PMID:26069265 | Free, Available for download, Freely available, | OMICS_21399 | https://sources.debian.org/src/r-cran-alakazam/ | SCR_024261 | 2026-09-19 12:56:21 | 6 | |||||||
|
ade4 Resource Report Resource Website 10+ mentions |
ade4 (RRID:SCR_024259) | software resource, software toolkit | Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table. | multivariate data analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-ade4/ | SCR_024259 | 2026-09-19 12:56:21 | 20 | |||||||||
|
psignifit Resource Report Resource Website 1+ mentions |
psignifit (RRID:SCR_024196) | software library, software resource, software toolkit | Software toolbox to fit psychometric functions and to test hypotheses about psychometric data. | fit psychometric functions, test hypotheses, psychometric data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/psignifit/ | SCR_024196 | 2026-09-19 12:56:19 | 3 | |||||||||
|
bridgedbr Resource Report Resource Website |
bridgedbr (RRID:SCR_024231) | software resource, software toolkit | Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files. | R functions, load identifier mapping databases in R, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-bridgedbr/ | SCR_024231 | 2026-09-19 12:56:20 | 0 | |||||||||
|
CNEr Resource Report Resource Website |
CNEr (RRID:SCR_024233) | software resource, software toolkit | Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements. | identification and advanced visualization of sets, conserved noncoding elements, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33013 | https://sources.debian.org/src/r-bioc-cner/ | SCR_024233 | 2026-09-19 12:56:20 | 0 | ||||||||
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genomeinfodb Resource Report Resource Website 1+ mentions |
genomeinfodb (RRID:SCR_024235) | software resource, software toolkit | Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order. | data and functions, translation between different chromosome sequence naming conventions, chromosome sequence naming conventions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-genomeinfodb/ | SCR_024235 | 2026-09-19 12:56:20 | 4 |
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