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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MAGI Resource Report Resource Website 10+ mentions |
MAGI (RRID:SCR_003360) | analysis service resource, production service resource, service resource, data analysis service | A web service for fast microRNA-Seq data analysis in a GPU infrastructure. | fastq, c, perl, php, software program, gpu/cuda |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:24907367 | OMICS_04636 | SCR_003360 | 2025-05-12 11:05:23 | 28 | |||||||||
|
ALOHOMORA Resource Report Resource Website 1+ mentions |
ALOHOMORA (RRID:SCR_009117) | ALOHOMORA | software resource, software application | Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, ms-window, linux, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154219, biotools:alohomora | https://bio.tools/alohomora | SCR_009117 | 2025-05-12 11:10:45 | 8 | ||||||||
|
EAGLET Resource Report Resource Website 1+ mentions |
EAGLET (RRID:SCR_009166) | EAGLET | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location. | gene, genetic, genomic, perl, c, linux, macos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154288 | SCR_009166 | Efficient Analysis of Genetic Linkage: Testing and Estimation | 2025-05-12 11:10:51 | 1 | |||||||
|
EASYLINKAGE/EASYLINKAGE-PLUS Resource Report Resource Website 1+ mentions |
EASYLINKAGE/EASYLINKAGE-PLUS (RRID:SCR_009167) | EASYLINKAGE/EASYLINKAGE-PLUS | software resource, software application | Software application that combines automated setup and performance of linkage analyses and simulation. The program package supports currently single-point linkage analyses, multi-point linkage analyses, and the simulation package SLink, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters. The software can analyze STRPs as well as SNP chip data from Affymetrix, Illumina, or self-defined SNP data. The program performs single- and multi-point simulation studies. | gene, genetic, genomic, perl, v5.8 (program can be provided as perl script or as a compiled exe for the use in windows), ms-windows, (2000/xp), linux | is listed by: Genetic Analysis Software | nlx_154289 | https://omictools.com/easylinkage-tool | http://compbio.charite.de/genetik/hoffmann/easyLINKAGE/ | SCR_009167 | 2025-05-12 11:10:51 | 5 | |||||||
|
HAPLOPOOL Resource Report Resource Website |
HAPLOPOOL (RRID:SCR_009225) | HAPLOPOOL | software resource, software application | Software program for estimating haplotype frequencies either from genotypes of individuals or from genotypes of pooled individuals. The genotypes must be for a block of bi-allelic SNPs (meaning that the SNPs should be in linkage disequilibrium with each other). The program assumes that it is given many genotypes of unrelated diploid individuals in Hardy-Weinberg equilibrium. If the genotypes are from pooled DNA, the program assumes that every pool contains the same number of individuals and the individuals were chosen at random when placed into the pools. For a reasonable running-time, the number of individuals in a pool needs to be between 2 and 4. (entry from Genetic Analysis Software) | gene, genetic, genomic, gcc/g++, perl, matlab | is listed by: Genetic Analysis Software | nlx_154382 | SCR_009225 | 2025-05-12 11:10:59 | 0 | |||||||||
|
EVOKER Resource Report Resource Website 1+ mentions |
EVOKER (RRID:SCR_009145) | EVOKER | software resource, software application | A graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies. It provides a solution to the computational and storage problems related to being able to work with the huge volumes of data generated by such projects by implementing a compact, binary format that allows rapid access to data, even with hundreds of thousands of observations. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, perl | is listed by: Genetic Analysis Software | nlx_154305 | SCR_009145 | 2025-05-12 11:10:49 | 8 | |||||||||
|
CCREL Resource Report Resource Website |
CCREL (RRID:SCR_009142) | CCREL | software resource, software application | Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, perl, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:ccrel, nlx_154261 | https://bio.tools/ccrel | SCR_009142 | Case-Control association analysis with RELlated individuals | 2025-05-12 11:10:48 | 0 | |||||||
|
POWERTRIM Resource Report Resource Website 1+ mentions |
POWERTRIM (RRID:SCR_009333) | POWERTRIM | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. Software application that automate the decision to remove objects from a pedigree with a minimum loss information (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | PMID:12677557 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154545 | SCR_009333 | 2025-05-12 11:11:04 | 1 | |||||||
|
GGSD Resource Report Resource Website |
GGSD (RRID:SCR_013129) | software resource, software application | Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, php, perl, web-based | is listed by: Genetic Analysis Software | nlx_154355 | SCR_013129 | Generic Genetic Studies Database | 2025-05-12 11:14:30 | 0 | |||||||||
|
BXH/XCEDE Tools Resource Report Resource Website 1+ mentions |
BXH/XCEDE Tools (RRID:SCR_009439) | BXH/XCEDE Tools | software resource, software application, image analysis software, data processing software | A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts. | analyze, c, c++, console (text based), dicom, format conversion, linux, macos, mgh/mgz, microsoft, minc, magnetic resonance, nifti, perl, posix/unix-like, quantification, sh/bash, statistical operation, unix shell, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Function BIRN |
BIRN License | nlx_155583 | SCR_009439 | 2025-05-12 11:11:09 | 4 | ||||||||
|
DOAF Resource Report Resource Website 1+ mentions |
DOAF (RRID:SCR_015666) | DOAF | portal, data or information resource, project portal, database | Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF). | disease ontology, annotation, collaboration, collaborative project, java, perl, rubby |
uses: Human Disease Ontology is related to: NUgene Project is related to: Gene Ontology is related to: OBO has parent organization: Northwestern University; Illinois; USA |
NCRR 1R01RR025342; CTSA UL1RR025741 |
PMID:23251346 | Public, Available for download, Tutorial Available | SCR_015666 | Disease Ontology Annotation Framework, Disease Ontology Annotation Framework (DOAF) | 2025-05-12 11:17:01 | 1 | ||||||
|
HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software resource, software application | 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 | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2025-05-12 11:03:39 | 44 | ||||||
|
RHMAPPER Resource Report Resource Website |
RHMAPPER (RRID:SCR_000845) | RHMAPPER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154576 | SCR_000845 | 2025-05-12 11:02:51 | 0 | ||||||||
|
BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software resource, software application | 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 | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2025-05-12 11:03:44 | 347 | |||||||
|
WIRM - Web Interfacing Repository Manager Resource Report Resource Website |
WIRM - Web Interfacing Repository Manager (RRID:SCR_002039) | software resource, software toolkit | WIRM is an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. WIRM reduces the complexity of building custom biomedical web applications and it's visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. WIRM is a Perl-based application server that provides a high-level programming environment for developing web information systems. WIRM consists of an object-relational database and a suite of Perl interfaces for visualizing, integrating and analyzing heterogeneous multimedia data. WIRM provides facilities for creating context-sensitive views over a multimedia database, allowing developers to rapidly build dynamic web sites that adapt their content and presentation to multiple classes of end-users. WIRM was developed by Rex Jakobovits as part of his PhD dissertation at the University of Washington Computer Science department, under the guidance of Dr. James F. Brinkley of the Department of Biological Structure. The system was generalized from work funded by NIH SBIR grant R43-MH61277-01 and Human Brain Project grant DC/LM02310. | application server, development tools, management systems, perl, programming environment, visual modeling, web applications | PMID:12386108 | nif-0000-11991 | SCR_002039 | WIRM | 2025-05-12 11:04:00 | 0 | |||||||||
|
MAPCREATOR Resource Report Resource Website 1+ mentions |
MAPCREATOR (RRID:SCR_008001) | MAPCREATOR | software resource, software application | Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | nlx_154455 | SCR_008001 | 2025-05-12 11:09:43 | 3 | |||||||||
|
ASPEX Resource Report Resource Website 1+ mentions |
ASPEX (RRID:SCR_008414) | ASPEX | software resource, software application | A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, tcl, perl, (the graphic script requires xmgr, available from ftp://ftp.teleport.com/pub/users/pturner/acegr), unix, (solaris/sunos/irix/osf-1), linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154234, biotools:aspex | https://bio.tools/aspex | SCR_008414 | Affected Sib Pairs EXclusion map | 2025-05-12 11:10:02 | 9 | |||||||
|
COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2025-04-19 06:43:31 | 18 | |||||
|
RINS Resource Report Resource Website 10+ mentions |
RINS (RRID:SCR_003652) | RINS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only. | virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perl |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22377895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00223 | SCR_003652 | 2025-04-19 06:41:48 | 26 | |||||||
|
PeaKDEck Resource Report Resource Website 10+ mentions |
PeaKDEck (RRID:SCR_004268) | PeaKDEck | software resource | A peak-calling software program for DNAseI-seq data. | perl, command line, gui |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:24407222 | OMICS_02207 | SCR_004268 | 2025-04-19 06:42:14 | 10 |
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