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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
AMOS Resource Report Resource Website 1000+ mentions |
AMOS (RRID:SCR_013067) | AMOS | software resource | A collection of tools and class interfaces for the assembly of DNA reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1093/bib/bbr074 | OMICS_00008, biotools:amos | https://bio.tools/amos, https://sources.debian.org/src/ampliconnoise/ | SCR_013067 | SciCrunch Registry | 2026-10-17 01:28:36 | 4855 | |||||||
|
Reptile Resource Report Resource Website 10+ mentions |
Reptile (RRID:SCR_013075) | Reptile | software resource | A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20834037 | biotools:reptile, OMICS_01109 | https://bio.tools/reptile | SCR_013075 | SciCrunch Registry | 2026-10-17 01:28:36 | 30 | |||||||
|
IUPHAR/BPS Guide to Pharmacology Resource Report Resource Website 1000+ mentions |
IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) | IUPHAR Database, IUPHAR-DB, IUPHAR GPCR, IUPHAR RECEPTOR | data or information resource, database, narrative resource, portal, standard specification | Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. | pharmacology, drug discovery, portal, guide, physiology, molecular structure, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: NC-IUPHAR |
Wellcome Trust | PMID:21087994 | nif-0000-03056, biotools:iuphar-db, r3d100013308 | https://bio.tools/iuphar-db, https://doi.org/10.17616/R31NJMRG | http://www.iuphar-db.org | SCR_013077 | SciCrunch Registry | International Union of Pharmacology Database, International Union of Basic and Clinical Pharmacology Database | 2026-10-17 01:28:40 | 2375 | ||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | SciCrunch Registry | 2026-10-17 01:28:49 | 320 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | SciCrunch Registry | Telescoper - De novo assembly algorithm | 2026-10-17 01:28:37 | 0 | ||||||
|
IsoLasso Resource Report Resource Website 1+ mentions |
IsoLasso (RRID:SCR_013176) | IsoLasso | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01320, biotools:isolasso | https://bio.tools/isolasso | SCR_013176 | SciCrunch Registry | 2026-10-17 01:28:41 | 3 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | SciCrunch Registry | heurAA - NGS multiplexed amplicon aligner | 2026-10-17 01:28:37 | 0 | ||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | SciCrunch Registry | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-10-17 01:28:49 | 1418 | ||||
|
MAP Resource Report Resource Website 1+ mentions |
MAP (RRID:SCR_013216) | software resource | This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., 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: Peking University; Beijing; China |
PMID:22495746 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01424, biotools:MAP | https://bio.tools/MAP | SCR_013216 | SciCrunch Registry | Metagenomic Assembly Program | 2026-10-17 01:28:48 | 1 | ||||||
|
PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | data analysis software, data processing software, simulation software, software application, software resource | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | SciCrunch Registry | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-10-17 01:28:48 | 4723 | |||||
|
ASHLAR Resource Report Resource Website 1+ mentions |
ASHLAR (RRID:SCR_016266) | Ashlar | data processing software, image processing software, software application, software resource | Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration. | cycif, registration, software, python, cyclic, immunofluorescence, fluorescence, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM107618 | Free, Available for download | biotools:ASHLAR | https://bio.tools/ASHLAR | SCR_016266 | SciCrunch Registry | ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration | 2026-10-17 01:29:10 | 6 | |||||
|
tensorflow Resource Report Resource Website 500+ mentions |
tensorflow (RRID:SCR_016345) | software library, software resource, software toolkit | Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. | high, performance, numerical, computation, machine, learning, framework, everyone, bio.tools |
is used by: transfer_ learning_ ccnn is listed by: Debian is listed by: bio.tools is related to: PPR-Meta is related to: PySyft is related to: Rosetta is related to: tf-encrypted |
Free, Available for download, Freely available | biotools:tensorflow | https://github.com/tensorflow/tensorflow, https://bio.tools/tensorflow, https://sources.debian.org/src/libtensorflow-framework2/ | SCR_016345 | SciCrunch Registry | 2026-10-17 01:29:11 | 724 | ||||||||
|
MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, data repository, portal, service resource, storage service resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
EMBL ; EU Seventh Framework Programme for Research MICROB3; InnovateUK 102513; Research Councils UK (RCUK) ; the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; the European Commission within the Research Infrastructures programme of Horizon 2020 676559 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | SciCrunch Registry | , MGnify, EBI Metagenomics | 2026-10-17 01:29:26 | 74 | |||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data analysis software, data processing software, software application, software resource | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | SciCrunch Registry | 2026-10-17 01:29:07 | 76 | ||||||||
|
Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | data analysis software, data processing software, data visualization software, software application, software resource | Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems. | alternative, splicing, analysis, next, generation, sequencing, data, transcriptome, identify, annotate, visualize, Perl, UNIX, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:26618088 | Free, Available for download, Freely available | biotools:splicing_express | https://bio.tools/splicing_express | SCR_016498 | SciCrunch Registry | 2026-10-17 01:29:07 | 3 | |||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | SciCrunch Registry | 2026-10-17 01:29:14 | 151 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | data analysis software, data processing software, software application, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit, https://bio.tools/transit | SCR_016492 | SciCrunch Registry | 2026-10-17 01:29:07 | 4 | |||||||
|
ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | data analysis software, data processing software, software application, software resource | Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders. | nonparametric, statistical, test, compare, clustering, structure, functional, brain, network, magnetic, resonance, imaging, data, fMRI, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: CRAN |
CAPES and CNPq Fellowships ; Ciência sem Fronteiras Fellowship ; NAP eScience ; Pew Latin American Fellowship ; State of São Paulo Research Foundation |
PMID:28174516 | Free, Available for download, Freely available | biotools:anocva | https://bio.tools/anocva | SCR_016719 | SciCrunch Registry | ANalysis Of Cluster VAriability, Analysis of Cluster Variability | 2026-10-17 01:29:32 | 0 | ||||
|
CARD Resource Report Resource Website 10+ mentions |
CARD (RRID:SCR_016602) | CARD | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, web application | Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data. | integrated, analysis, interactive, visualization, RNA, interfernce, screening, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Australasian Genomics Technologies Association ; Australian Cancer Research Foundation ; Australian Government’s Education Investment Fund ; Brockhoff Foundation ; Peter MacCallum Cancer Centre Foundation ; Victorian Department of Industry ; Innovation and Regional Development |
PMID:26902267 | Free, Freely available | biotools:CARD | https://bio.tools/CARD | SCR_016602 | SciCrunch Registry | CARD, Comprehensive Analysis of RNAi-screen Data | 2026-10-17 01:29:08 | 20 | ||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Canadian Institutes of Health Research (CIHR) and Genome BC ; Michael Smith Foundation for Health Research ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | SciCrunch Registry | VisRseq, VisR | 2026-10-17 01:29:08 | 5 |
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