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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MethBase Resource Report Resource Website 1+ mentions |
MethBase (RRID:SCR_017487) | data or information resource, database, service resource | Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics. | Methylome, database, public, BSseq, dataset, methylation, site, region, allele, specific, metadata, statistics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
Free, Freely available | BioTools:MethBase, biotools:Methbase | https://bio.tools/MethBase, https://bio.tools/MethBase, https://bio.tools/MethBase | SCR_017487 | MethBase: a reference methylome database | 2026-09-19 12:57:36 | 1 | |||||||
|
Signaling Pathways Project Resource Report Resource Website 10+ mentions |
Signaling Pathways Project (RRID:SCR_018412) | SPP | data or information resource, database | Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available. | Data integration, genetic database, gene regulatory network, cell signalling, cellular signalling network, transcriptomic data, manualy curated, cistromic data, cellular receptor, enzyme, transcrptomic factor, mammalian cellular signaling pathway, data mining strategy, dataset, , bio.tools |
is used by: Hypothesis Center is listed by: Debian is listed by: bio.tools works with: Gene Expression Omnibus (GEO) works with: NCBI Sequence Read Archive (SRA) |
CPRIT RP150578; Dan L. Duncan NCI Comprehensive Cancer Center at Baylor College of Medicine ; NCI CA125123; NHLBI HL127624; NIDDK DK095686; NIDDK DK097748; NIDDK DK097771; NIDDK DK105126; NIDDK DK107535; NIDDK DK48807; NIDDK DK56338 |
PMID:31672983 | Free, Freely available | r3d100013650, biotools:Signaling_Pathways_Project | https://bio.tools/Signaling_Pathways_Project, https://doi.org/10.17616/R31NJN0Y | https://www.signalingpathways.org | SCR_018412 | 2026-09-19 12:57:37 | 34 | ||||
|
VeryFastTree Resource Report Resource Website 1+ mentions |
VeryFastTree (RRID:SCR_023594) | software application, software resource, source code | Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies. | large alignments, phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: bio.tools is related to: FastTree |
ERDF ; MICINN ; Xunta de Galicia |
PMID:32573652 DOI:10.1093/bioinformatics/btaa582 |
Free, Available for download, Freely available | biotools:veryfasttree | https://bio.tools/veryfasttree | SCR_023594 | 2026-09-19 12:57:39 | 8 | ||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-09-19 12:57:41 | 0 | ||||||
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FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software application, software resource | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (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:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | FLexible Ordered SubSet analysis | 2026-09-19 12:57:42 | 0 | |||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-09-19 12:57:40 | 0 | ||||||
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mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-09-19 12:57:41 | 5 | |||||||
|
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 | 2026-09-19 12:57:44 | 17 | |||||
|
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 | 2026-09-19 12:57:44 | 44 | ||||
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software application, software resource, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Cancer Research UK ; Erik and Edith Fernström foundation |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-09-19 12:57:43 | 0 | ||||||
|
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 | 2026-09-19 12:57:44 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-09-19 12:57:44 | 301 | ||||||
|
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 | 2026-09-19 12:57:46 | 20 | |||||
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mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-09-19 12:55:49 | 0 | ||||||
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SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | data processing software, software application, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-09-19 12:55:49 | 403 | |||||
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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 | 2026-09-19 12:58:06 | 401 | ||||||||
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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 | 2026-09-19 12:58:06 | 287 | ||||||||
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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 | 2026-09-19 12:58:03 | 0 | ||||||||
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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 | 2026-09-19 12:58:03 | 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 | 2026-09-19 12:58:05 | 1 |
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