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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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METAL Resource Report Resource Website 1000+ mentions |
METAL (RRID:SCR_002013) | software application, software resource | Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software) | gene, genetic, genomic, whole genome |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:20616382 | nlx_154476, OMICS_00239 | SCR_002013 | Metal - Meta Analysis Helper, METa AnaLysis Helper | 2026-09-12 01:02:27 | 2413 | ||||||||
|
Partners HealthCare Biobank Resource Report Resource Website 1+ mentions |
Partners HealthCare Biobank (RRID:SCR_001316) | biomaterial supply resource, material resource | Blood biobank for the Partners research program, which investigates the affects of genes, lifestyle and environment on human health. | biology, biobank, specimen, research, gene, lifestyle, environment, blood | Free, Freely Available | nlx_31066 | https://biobank.partners.org | http://www.partners.org/researchcores/DFHCC/virtual_specimen_DFHCC.html | SCR_001316 | 2026-09-12 01:02:26 | 4 | ||||||||
|
SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | commercial organization, software application, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-09-12 01:02:27 | 17 | |||||
|
IBA GmbH Resource Report Resource Website 1+ mentions |
IBA GmbH (RRID:SCR_001132) | biomaterial supply resource, material resource | A commercial company that provides a range of services from nucleic acid custom services to products and services for cloning, transfection, recombinant protein production and cell isolation. | nucleic acid, antibody, cloning, gene, genomics, research, biomaterial supply resource | nlx_152379 | SCR_001132 | 2026-09-12 01:02:25 | 2 | |||||||||||
|
LAMBDAA Resource Report Resource Website |
LAMBDAA (RRID:SCR_001128) | LAMBDAA | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154421 | SCR_001128 | 2026-09-12 01:02:25 | 0 | ||||||||
|
CAROL Resource Report Resource Website 10+ mentions |
CAROL (RRID:SCR_001800) | CAROL | software application, software resource | Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system. | gene, genetic, genomic, r, prediction, non-synonymous coding variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22261837 | Free, Available for download, Freely available | nlx_154254, OMICS_00143 | http://www.sanger.ac.uk/resources/software/carol/ | SCR_001800 | Combined Annotation scoRing toOL | 2026-09-12 01:02:26 | 11 | |||||
|
LDMET Resource Report Resource Website 1+ mentions |
LDMET (RRID:SCR_001127) | LDMET | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154027 | SCR_001127 | 2026-09-12 01:02:25 | 1 | ||||||||
|
CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software application, software resource | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-09-12 01:02:26 | 1960 | ||||||
|
POLYMUTT Resource Report Resource Website 1+ mentions |
POLYMUTT (RRID:SCR_002051) | Polymutt | software application, software resource | Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation sequencing, mutation, de novo point mutation, single nucleotide variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:23055937 | Free, Available for download, Freely available | OMICS_00088, nlx_154539 | SCR_002051 | POLYmorphism and de novo MUTaTion call in families with sequencing data | 2026-09-12 01:02:27 | 3 | ||||||
|
EIGENSOFT/EIGENSTRAT Resource Report Resource Website 1+ mentions |
EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) | EIGENSOFT/EIGENSTRAT | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, linux | is listed by: Genetic Analysis Software | Free, Available for download, Freely available | nlx_154296 | http://www.hsph.harvard.edu/faculty/alkes-price/software/ | SCR_001357 | 2026-09-12 01:02:26 | 3 | |||||||
|
BIRDSUITE Resource Report Resource Website 10+ mentions |
BIRDSUITE (RRID:SCR_001794) | Birdsuite | software application, software resource | Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs. | gene, genetic, genomic, snp, genotype, copy number polymorphism, copy number variant, affymetrix |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Broad Institute |
PMID:18776909 | Free, Available for download, Freely available | OMICS_00705, nlx_154245 | SCR_001794 | 2026-09-12 01:02:26 | 43 | |||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-09-12 01:02:26 | 44 | ||||
|
PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-09-12 01:02:27 | 17 | ||||||
|
MapMan Resource Report Resource Website 1000+ mentions |
MapMan (RRID:SCR_003543) | MapMan | software application, software resource | Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes. | metabolic pathway, biological process, genomics, pathway, array, visualization, gene, transcript, protein, enzyme, metabolite |
is related to: GoMapMan has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany |
PMID:19389052 PMID:14996223 PMID:16009995 PMID:16649112 |
nlx_157682 | SCR_003543 | MapMan Application Software | 2026-09-12 01:02:30 | 1251 | |||||||
|
IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine. | gene, analysis, domain, homology, immunoglobulin v, nucleotide, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: NCBI |
PMID:23671333 | Free, Freely available | nif-0000-25554, biotools:igblast, OMICS_06083 | https://bio.tools/igblast, https://sources.debian.org/src/ncbi-igblast/ | SCR_002873 | IgBLAST | 2026-09-12 01:02:29 | 625 | ||||||
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Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders Resource Report Resource Website 1+ mentions |
Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders (RRID:SCR_003282) | Pleiades Promoter Project | biomaterial supply resource, material resource | Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy. | Human, DNA, promoter, gene, expression, brain, disorder, therapy |
is listed by: One Mind Biospecimen Bank Listing is related to: CanEuCre is related to: JAX Cre Repository is related to: Recombinase (cre) Activity has parent organization: University of British Columbia; British Columbia; Canada |
Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, Cancer | Child and Family Research Institute ; Genome British Columbia ; Genome Canada ; UBC Institute of Mental Health |
Free, Freely available | nif-0000-01868 | https://plone.bcgsc.ca/project/pleiades-promoter-project | http://www.pleiades.org/ | SCR_003282 | 2026-09-12 01:02:29 | 4 | ||||
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Multipoint Identical-by-descent Method Resource Report Resource Website |
Multipoint Identical-by-descent Method (RRID:SCR_004676) | MIM | software application, software resource | Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | PMID:9433587 | nlx_154482 | SCR_004676 | 2026-09-12 01:02:33 | 0 | ||||||||
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PEDSCRIPT Resource Report Resource Website |
PEDSCRIPT (RRID:SCR_004571) | PEDSCRIPT | software application, software resource | Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154528 | SCR_004571 | 2026-09-12 01:02:33 | 0 | |||||||||
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SepNet Central Sample Bank Resource Report Resource Website |
SepNet Central Sample Bank (RRID:SCR_004543) | SepNetBiobank | biomaterial supply resource, material resource | It is the aim of the SepNet initiative to establish a central facility, essential to data and sample quality and homogeneity, that comprises a structured and easily accessible sample bank with probes of homogeneous quality originating from a well-characterized patient population enrolled in independent, innovative and internationally competitive prospective clinical sepsis trials. The SepNetBiobank is a core facility of SepNet. The object of this central sample resource is to organize and handle all relevant aspects of sampling, storage and delivery of samples in the SepNet collaboration to ensure homogeneity of the samples in terms of specimen quality and maintaining sampling standards. This will be achieved through central handling of samples collected in peripheral nationwide 17 regional centers and an additional 36 associated centers according to an agreed sampling scheme and pre-set standards for sample quality, sample handling and banking; quality assurance and all relevant parts of sample handling will be in the hands of the core unit, minimizing pre-analytical steps in the heterogeneous environment of the different regional centers. In the next few months a fully automated sample storage system will be implemented that allows handling of more than 200.000 individual aliquots expected after completion of the different ongoing and planned SepNet Trails. In the next six months a fully automated -80 degree C sample storage system will be implemented. After completion of the plannend and ongoing SepNet trials more than 59.710 expected primary samples (218.040 aliquots) will be stored in this system. This outstanding sample resource will provide the basis for scientific projects aming at improving patient care with sepsis e.g. advancement in diagnostics, risk stratification, therapy and outcome. | dna, peripheral blood, blood, serum, plasma, infectious disease, sepsis, infection, parasitic disease, disease, parasite, clinical sepsis trial, clinical, gene, gene expression, phenotype, frozen, clinical trial | is listed by: One Mind Biospecimen Bank Listing | Infectious disease, Sepsis, Infection, Parasitic disease, Disease | German Federal Ministry of Research and Education | Collaborators / Public?: The object of this central sample resource is to organize and handle all relevant aspects of sampling, Storage and delivery of samples in the SepNet collaboration to ensure homogeneity of the samples in terms of specimen quality and maintaining sampling standards. This outstanding sample resource will provide the basis for scientific projects aming at improving patient care with sepsis e.g. advancement in diagnostics, Risk stratification, Therapy and outcome. | nlx_53583 | http://www.tmf-ev.de/Arbeitsgruppen_Foren/AGBMB.aspx | SCR_004543 | Biobank Kompetenznetz Sepsis | 2026-09-12 01:02:33 | 0 | ||||
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PEDPLOT Resource Report Resource Website |
PEDPLOT (RRID:SCR_003843) | PEDPLOT | software application, software resource | Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, postscript, unix, (sparc-solaris 2.5/dec unix 4.0/x86-solaris 2.6) | is listed by: Genetic Analysis Software | nlx_154526 | SCR_003843 | 2026-09-12 01:02:31 | 0 |
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