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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
EpiDISH R package Resource Report Resource Website 10+ mentions |
EpiDISH R package (RRID:SCR_018004) | EpiDISH | software resource, software toolkit | Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. | Epigenetic, sample heterogeneity, reference, algorithm, correcting, cell type, bio.tools |
is listed by: bio.tools is listed by: Debian |
Chinese Academy of Sciences ; EU-FP7 ; Max-Planck Society ; NSFC 31571359; Royal Society Newton Advanced Fellowship ; Shanghai Institute for Biological Sciences |
PMID:28193155 | Free, Available for download, Freely available | biotools:epidish | https://github.com/sjczheng/EpiDISH, https://bio.tools/epidish | SCR_018004 | Epigenetic Dissection of Intra-Sample Heterogeneity | 2026-09-03 05:05:07 | 14 | ||||
|
FaceSync Resource Report Resource Website |
FaceSync (RRID:SCR_021396) | software resource, software toolkit | Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras. | Automatically synchronize videos, manually align audio, plot facial landmark movements, graph data, head mounted camera setup, 3D blueprints, recording facial expressions, OpenBehavior, Bio.Tools |
is listed by: OpenBehavior is related to: FaceSync project |
PMID:32185017 | Free, Available for download, Freely Available | biotools:FaceSync | https://edspace.american.edu/openbehavior/project/facesync/, https://bio.tools/FaceSync | SCR_021396 | 2026-09-03 05:05:19 | 0 | |||||||
|
SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, data processing software, software application, software resource | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Health ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-09-03 04:50:15 | 31 | ||||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, data processing software, software application, software resource | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach, https://bio.tools/mach | https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-09-03 04:50:01 | 937 | |||||
|
iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-09-03 04:50:11 | 11 | ||||||
|
SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-09-03 04:50:17 | 21 | |||||||
|
IsoEM Resource Report Resource Website 10+ mentions |
IsoEM (RRID:SCR_009993) | IsoEM | software resource | Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Connecticut; Connecticut; USA |
biotools:isoem, OMICS_01278 | https://bio.tools/isoem | SCR_009993 | 2026-09-03 04:50:13 | 10 | ||||||||
|
BitSeq Resource Report Resource Website 10+ mentions |
BitSeq (RRID:SCR_009904) | BitSeq | software resource | A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btv483 DOI:10.1093/bioinformatics/bts260 |
, OMICS_01269, biotools:bitseq | https://bio.tools/bitseq, https://sources.debian.org/src/bitseq/, | SCR_009904 | 2026-09-03 04:50:18 | 20 | |||||||
|
BEAST Resource Report Resource Website 5000+ mentions |
BEAST (RRID:SCR_010228) | data analysis software, data processing software, sequence analysis software, software application, software repository, software resource | A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. | bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: TempEst is related to: BEAST2 is related to: PhyDyn has parent organization: University of Edinburgh; Scotland; United Kingdom |
DOI:10.1186/1471-2148-7-214 | nlx_156859, OMICS_04233, biotools:beast, SCR_015988 | http://www.nitrc.org/projects/beast-library, https://bio.tools/beast, https://sources.debian.org/src/beast-mcmc/ | http://beast.bio.ed.ac.uk/Main_Page | SCR_010228 | BEaST Segmentation Library, Beast Software | 2026-09-03 04:50:19 | 6777 | ||||||
|
WEBLOGO Resource Report Resource Website 1000+ mentions |
WEBLOGO (RRID:SCR_010236) | data access protocol, service resource, software resource, web service | Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. | Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI K22 HG00056; NIGMS P50 GM62412; Searle Scholars program |
PMID:15173120 | Free, Available for download, Freely available | nlx_156853, biotools:weblogo_3 | http://weblogo.threeplusone.com/, https://bio.tools/weblogo_3 | SCR_010236 | WebLogo Version 2.8.2, WebLogo3, WebLogo | 2026-09-03 04:50:06 | 3980 | |||||
|
MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-09-03 04:50:48 | 468 | |||||||
|
Pathema Resource Report Resource Website 1+ mentions |
Pathema (RRID:SCR_010585) | Pathema | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. | bacillus anthracis, clostridium botulinum, burkholderia mallei, burkholderia pseudomallei, clostridium perfringens, entamoeba histolytica, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
NIAID contract HHSN266200400038C | PMID:19843611 | biotools:pathema, nlx_45829 | https://bio.tools/pathema | SCR_010585 | Pathema Genome Resource, Pathema Bioinformatics Resource Center | 2026-09-03 04:50:32 | 6 | |||||
|
icy Resource Report Resource Website 100+ mentions |
icy (RRID:SCR_010587) | ICY | data processing software, image analysis software, image processing software, service resource, software application, software development environment, software development tool, software repository, software resource, source code | An open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download. | image analysis, microscopy, javascript, python, plugin, protocol, script, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Pasteur Institute |
Centre National de la Recherche Scientifique ; French National Research Agency ANR-10-INBS-04-06 |
PMID:22743774 | Free, Open unspecified license, GNU General Public License, v3, The community can contribute to this resource | biotools:icy, nlx_45928 | https://bio.tools/icy | SCR_010587 | icy bioimage analysis | 2026-09-03 04:50:19 | 355 | ||||
|
Geneious Resource Report Resource Website 10000+ mentions |
Geneious (RRID:SCR_010519) | data analysis software, data management software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. | Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is parent organization of: Geneious Microsatellite Plugin |
PMID:22543367 | Restricted | OMICS_00016, biotools:geneious | http://nebc.nerc.ac.uk/news/geneiousonbl, https://bio.tools/geneious | SCR_010519 | Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic | 2026-09-03 04:50:45 | 13589 | ||||||
|
CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | 2026-09-03 04:50:36 | 8 | ||||||||
|
Relate Resource Report Resource Website 10+ mentions |
Relate (RRID:SCR_010794) | Relate | software resource | Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19025785 | biotools:relateadmix, OMICS_00207 | https://bio.tools/relateadmix | SCR_010794 | 2026-09-03 04:50:40 | 47 | |||||||
|
tRNAscan-SE Resource Report Resource Website 1000+ mentions |
tRNAscan-SE (RRID:SCR_010835) | tRNAscan-SE | software resource, production service resource, service resource, analysis service resource, data analysis service | Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of California at Santa Cruz; California; USA |
PMID:15980563 PMID:9023104 DOI:10.1093/nar/25.5.0955 |
Acknowledgement requested | OMICS_00385, biotools:trnascan-se | https://bio.tools/trnascan-se, https://sources.debian.org/src/trnascan-se/ | SCR_010835 | 2026-09-03 04:50:55 | 1695 | ||||||
|
MoDIL Resource Report Resource Website 1+ mentions |
MoDIL (RRID:SCR_010764) | MoDIL | software resource | Software for a novel method for finding medium sized indels from high throughput sequencing datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
OMICS_00066, biotools:modil | https://bio.tools/modil | SCR_010764 | MoDIL: Detecting INDEL Variation with Clone-end Sequencing | 2026-09-03 04:50:38 | 4 | |||||||
|
MISA Resource Report Resource Website 1000+ mentions |
MISA (RRID:SCR_010765) | MISA | software resource | Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00110, biotools:misa | https://bio.tools/misa | SCR_010765 | MISA - MIcroSAtellite identification tool | 2026-09-03 04:50:24 | 1053 | |||||||
|
GensearchNGS Resource Report Resource Website 10+ mentions |
GensearchNGS (RRID:SCR_010802) | GensearchNGS | software resource | An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Commercial license | OMICS_00287, biotools:gensearchngs | https://bio.tools/gensearchngs | SCR_010802 | 2026-09-03 04:50:53 | 23 |
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