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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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zAlign Resource Report Resource Website |
zAlign (RRID:SCR_024360) | aligment software | Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs. | sequence aligner, large biological DNA sequences, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21299 | https://sources.debian.org/src/zalign/ | SCR_024360 | zalign | 2026-07-25 12:10:36 | 0 | |||||||
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iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-07-25 12:10:24 | 0 | ||||||
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FANTOM DB Resource Report Resource Website 10+ mentions |
FANTOM DB (RRID:SCR_002678) | FANTOM DB | biomaterial supply resource, material resource | The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN. | cdna clone, mouse, mouse cdna, human, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: CAGE has parent organization: RIKEN Omics Science Center |
PMID:20211142 | Free, Available for download, Freely available | nif-0000-02833, biotools:fantom | http://fantom3.gsc.riken.jp/, https://bio.tools/fantom | SCR_002678 | FANTOM: Functional Annotation of Mouse, FANTOM2, FANTOM1, Functional Annotation of the Mammalian Genome, FANTOM4, FANTOM3, FANTOM, Functional Annotation of Mouse | 2026-07-25 12:12:24 | 20 | |||||
|
zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NIGMS GM63904; NIDA DA14546; NHGRI HG006431 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-07-25 12:12:37 | 4 | ||||
|
SKAT Resource Report Resource Website 100+ mentions |
SKAT (RRID:SCR_009396) | software application, software resource | Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154634, biotools:skat | https://bio.tools/skat | SCR_009396 | SNP-set (Sequence) Kernel Association Test | 2026-07-26 09:04:50 | 273 | ||||||||
|
MULTIDISEQ Resource Report Resource Website |
MULTIDISEQ (RRID:SCR_009304) | MULTIDISEQ | software application, software resource | A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154494, biotools:multidiseq | https://bio.tools/multidiseq | SCR_009304 | 2026-07-26 09:04:48 | 0 | ||||||||
|
MPDA Resource Report Resource Website 10+ mentions |
MPDA (RRID:SCR_009303) | MPDA | software application, software resource | A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlabr, ms-windows, (windows98/2000/xp), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:mpda, nlx_154492 | https://bio.tools/mpda | SCR_009303 | Microarray Pooled DNA Analyser | 2026-07-26 09:04:58 | 12 | |||||||
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SIMPED Resource Report Resource Website 1+ mentions |
SIMPED (RRID:SCR_009388) | software application, software resource | Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, ms-window, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:simped, nlx_154627 | https://bio.tools/simped | http://www.hgsc.bcm.tmc.edu/genemapping | SCR_009388 | 2026-07-26 09:05:01 | 1 | ||||||||
|
SIBLINK Resource Report Resource Website |
SIBLINK (RRID:SCR_009381) | software application, software resource | Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:siblink, nlx_154616 | https://bio.tools/siblink | http://wwwchg.duhs.duke.edu/software/siblink.html | SCR_009381 | 2026-07-26 09:04:49 | 0 | ||||||||
|
PRESTO: Genetic Association Analysis Software Resource Report Resource Website 1+ mentions |
PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) | software application, software resource | Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data. | gene, genetic, genomic, java, ms-windows, unix, solaris, linux, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu138 | nlx_154549 | SCR_013285 | 2026-07-26 09:05:51 | 2 | |||||||||
|
SWEEP Resource Report Resource Website 10+ mentions |
SWEEP (RRID:SCR_009418) | SWEEP | software application, software resource | Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:sweep, nlx_154667 | https://bio.tools/sweep | SCR_009418 | 2026-07-26 09:04:50 | 32 | ||||||||
|
SUMSTAT Resource Report Resource Website 10+ mentions |
SUMSTAT (RRID:SCR_009416) | software application, software resource | Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, free pascal, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154663, biotools:sumstat | https://bio.tools/sumstat | SCR_009416 | 2026-07-26 09:04:50 | 11 | |||||||||
|
SUP Resource Report Resource Website |
SUP (RRID:SCR_009417) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with trait locus. entry from Genetic Analysis Software. | gene, genetic, genomic, c, c++, unix, linux, cygwin, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is related to: SLINK is related to: FASTSLINK is related to: bio.tools |
PMID:16803631 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154664, biotools:sup | https://bio.tools/sup | SCR_009417 | Slink Utility Program | 2026-07-26 09:05:02 | 0 | ||||||
|
SASGENE Resource Report Resource Website |
SASGENE (RRID:SCR_013084) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (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 | biotools:sasgene, nlx_154608 | https://bio.tools/sasgene | SCR_013084 | 2026-07-26 09:05:49 | 0 | ||||||||
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SNPTEST Resource Report Resource Website 100+ mentions |
SNPTEST (RRID:SCR_009406) | software application, software resource | Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154651, biotools:snptest | https://bio.tools/snptest | http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html | SCR_009406 | 2026-07-26 09:04:50 | 396 | ||||||||
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TASSEL Resource Report Resource Website 1000+ mentions |
TASSEL (RRID:SCR_012837) | TASSEL | software application, software resource | Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, web-based, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
nlx_154674, biotools:tassel | http://sourceforge.net/projects/tassel/, https://bio.tools/tassel | SCR_012837 | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-07-26 09:05:47 | 2335 | |||||||
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ECLIPSE Resource Report Resource Website 100+ mentions |
ECLIPSE (RRID:SCR_013130) | software application, software resource | A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, tested on, unix, (compaq tru64 v5.0a), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154290, biotools:eclipse | https://bio.tools/eclipse | SCR_013130 | Error Correcting Likelihoods In Pedigree Structure Estimation. PANGAEA | 2026-07-26 09:05:50 | 121 | ||||||||
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SNP HITLINK Resource Report Resource Website |
SNP HITLINK (RRID:SCR_013340) | SNP HITLINK | software application, software resource | Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154644, biotools:snp_hitlink | https://bio.tools/snp_hitlink | SCR_013340 | SNP HIgh-Throughput LINKage analysis system | 2026-07-26 09:05:52 | 0 | |||||||
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THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software application, software resource | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-07-26 09:05:52 | 51 | |||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-07-26 09:06:37 | 4 |
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