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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DCTD Resource Report Resource Website 10+ mentions |
DCTD (RRID:SCR_004196) | DCTD | portal, data or information resource, funding resource | Division of NCI that takes prospective cancer detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging tests, and other therapeutic interventions (radiation, surgery, immunotherapy) in patients. DCTD, like all of NCI, supports many programs that could not be done without government funding - investigators supported by the division engage in scientifically sound, high-risk research that may yield great benefits for patients with cancer, but are too difficult or risky for industry or academia to pursue. This includes a particular emphasis on the development of distinct molecular signatures for cancer, refined molecular assays, and state-of-the-art imaging techniques that will guide oncologic therapy in the future. The division has eight major programs that work together to bring unique molecules, diagnostic tests, and therapeutic interventions from the laboratory bench to the patient bedside: * Cancer Diagnosis Program * Cancer Imaging Program * Cancer Therapy Evaluation Program * Developmental Therapeutics Program * Radiation Research Program * Translational Research Program * Biometrics Research Branch * Office of Cancer Complementary and Alternative Medicine | treatment, diagnosis, molecule, diagnostic test, therapeutic intervention |
is listed by: OMICtools has parent organization: National Cancer Institute is parent organization of: CDP |
Cancer | NCI | OMICS_01537 | SCR_004196 | Division of Cancer Treatment and Diagnosis | 2026-08-06 09:26:03 | 18 | ||||||
|
IMG System Resource Report Resource Website 100+ mentions |
IMG System (RRID:SCR_002965) | IMG, IMG/M | portal, data or information resource | Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets. | microbiome, microbial genetics, genome and metagenome datasets analysis, genome and metagenome datasets, genome, metagenomics, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Human Microbiome Project has parent organization: DOE Joint Genome Institute |
PMID:17932063 PMID:22086953 |
Free, Freely available | nif-0000-03010, OMICS_01478, SCR_014605, biotools:img_m | http://img.jgi.doe.gov/m, https://bio.tools/img_m | SCR_002965 | Integrated Microbial Genomes System | 2026-08-06 09:25:46 | 199 | |||||
|
SPInDel Resource Report Resource Website 1+ mentions |
SPInDel (RRID:SCR_004509) | SPInDel | data set, data or information resource, software resource | A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species. | virus, indel, dna barcoding, alignment, nucleotide sequence, visualization, conserved region, pcr primer, phylogenetic, variant |
is listed by: OMICtools has parent organization: University of Porto; Porto; Portugal has parent organization: SourceForge |
PMID:22978681 PMID:20923781 |
Acknowledgement requested, Free, Public | OMICS_01496 | SCR_004509 | SPecies Identification by Insertions/Deletions, SPInDel - Species identification by insertions/deletions | 2026-08-06 09:26:09 | 2 | ||||||
|
UCSF Spot Resource Report Resource Website 1+ mentions |
UCSF Spot (RRID:SCR_002985) | image analysis software, software application, data processing software, software resource | Automatic software program for microarray image quantification. | image quantification, microarray analysis |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Available to the academic community, Available to non-profit researchers | OMICS_00849 | SCR_002985 | 2026-08-06 09:25:46 | 2 | |||||||||
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American College of Medical Genetics and Genomics Resource Report Resource Website 50+ mentions |
American College of Medical Genetics and Genomics (RRID:SCR_005769) | ACMG | portal, data or information resource, organization portal | An organization composed of biochemical, clinical, cytogenetic, medical and molecular geneticists, genetic counselors and other health care professionals committed to the practice of medical genetics to Improve Health Through Medical Genetics. The American College of Medical Genetics and Genomics will: * Define and promote excellence in the practice of medical genetics and genomics in the integration of translational research into practice; * Promote and provide medical genetics and genomics education; * Increase access to medical genetics and genomics services and integrate them into patient care; * Advocate for and represent providers of medical genetics and genomics services and their patients; and * Maintain structure and integrity of ACMG and its value to members and the public. | genetics, genomics, medical, biochemical, clinical, cytogenetic, molecular, geneticist, genetic counselor, health care professional, medical genetics | is listed by: OMICtools | PMID:21311339 | OMICS_01775, nlx_149234 | http://www.acmg.net | SCR_005769 | American College of Medical Genetics, ACMG - Translating Genes Into Health, American College of Medical Genetics Genomics | 2026-08-06 09:26:24 | 50 | ||||||
|
Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | software application, commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-08-06 09:27:08 | 1 | ||||||||
|
Orphanet Resource Report Resource Website 100+ mentions |
Orphanet (RRID:SCR_006628) | Orphanet | portal, data or information resource | European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases. | drug, clinical, diagnostic, test, rare, disease, molecule, gene, orphan, drug |
is used by: NIF Data Federation is used by: HmtPhenome is listed by: OMICtools is related to: Disease core ontology applied to Rare Diseases is related to: phenomeNET has parent organization: National Institute of Health and Medical Research; Rennes; France is parent organization of: Orphanet Rare Disease Ontology |
National Institute of Health and Medical Research ; Rennes ; France ; French Directorate General for Health ; European Union |
Free, Freely available | nif-0000-21306, grid.458406.b, Wikidata: Q1515833 | https://ror.org/03d3kf570 | SCR_006628 | 2026-08-06 09:26:38 | 404 | ||||||
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COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | software application, data processing software, software resource | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-08-06 09:27:09 | 164 | ||||||
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epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | software application, data processing software, software resource | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-08-06 09:26:34 | 2 | |||||
|
SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-08-06 09:26:21 | 322 | ||||||
|
Subread Resource Report Resource Website 1000+ mentions |
Subread (RRID:SCR_009803) | software application, data processing software, software resource | Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread. | read alignment, DNA-seq reads mapping, RNA-seq reads mapping, mutation discovery, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Rsubread has parent organization: University of Melbourne; Victoria; Australia |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Freely available | OMICS_01255, biotools:subread | https://bio.tools/subread, https://sources.debian.org/src/subread/ | SCR_009803 | 2026-08-06 09:27:21 | 1854 | ||||||
|
Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | software application, data processing software, software resource | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-08-06 09:27:48 | 6255 | ||||||
|
TiltPicker Resource Report Resource Website |
TiltPicker (RRID:SCR_016674) | software application, data processing software, software resource | Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing. | particle, selection, single, electron, microscopy, interactive, graphical, interface, tilted, pair, dataset, image, processing | is listed by: OMICtools | NCRR RR23093; NCRR RR17573 |
PMID:19374019 | Free, Available for download, Freely available | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | SCR_016674 | 2026-08-06 09:28:56 | 0 | |||||||
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NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | software application, data processing software, software resource | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-08-06 09:28:59 | 268 | |||||||||
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ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | software application, data processing software, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-08-06 09:28:57 | 1 | ||||||
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Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | software application, data processing software, software resource | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Croatian Science Foundation ; Croatian Academy of Sciences and Arts ; A*STAR ; Singapore |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-08-06 09:29:10 | 149 | ||||||
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | standalone software, software application, data processing software, software resource | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-08-06 09:29:07 | 1309 | |||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | software application, data processing software, software resource | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-08-06 09:29:07 | 2 | |||||
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GeSeq Resource Report Resource Website 100+ mentions |
GeSeq (RRID:SCR_017336) | software application, service resource, data processing software, software resource | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-08-06 09:29:03 | 375 | ||||||
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NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects Resource Report Resource Website |
NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) | NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects | portal, project portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV | genome, sequencing |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_003205 | 2026-08-06 09:25:49 | 0 |
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