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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MapSplice Resource Report Resource Website 100+ mentions |
MapSplice (RRID:SCR_010844) | MapSplice | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Kentucky; Kentucky; USA |
PMID:20802226 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mapsplice, OMICS_01243 | https://bio.tools/mapsplice | SCR_010844 | SciCrunch Registry | 2026-09-19 12:52:00 | 214 | ||||||
|
QSRA Resource Report Resource Website 1+ mentions |
QSRA (RRID:SCR_010733) | QSRA | software resource | A quality-value guided de novo short read assembler. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00026, biotools:qsra | https://bio.tools/qsra | SCR_010733 | SciCrunch Registry | 2026-09-19 12:51:58 | 1 | ||||||||
|
HARSH Resource Report Resource Website 10+ mentions |
HARSH (RRID:SCR_010792) | HARSH | software resource | Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
OMICS_00199, biotools:harsh | https://bio.tools/harsh | SCR_010792 | SciCrunch Registry | HAplotype inference using Reference and Sequencing tecHnology | 2026-09-19 12:51:59 | 15 | |||||||
|
HapFABIA Resource Report Resource Website 1+ mentions |
HapFABIA (RRID:SCR_010793) | HapFABIA | software resource | Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:24174545 | biotools:hapfabia, OMICS_00203 | https://bio.tools/hapfabia | SCR_010793 | SciCrunch Registry | HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data | 2026-09-19 12:51:59 | 3 | ||||||
|
Pedimap Resource Report Resource Website 10+ mentions |
Pedimap (RRID:SCR_010796) | Pedimap | software resource | A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23087384 | OMICS_00214, biotools:pedimap | https://bio.tools/pedimap | SCR_010796 | SciCrunch Registry | 2026-09-19 12:51:59 | 11 | |||||||
|
CEQer Resource Report Resource Website 1+ mentions |
CEQer (RRID:SCR_010813) | CEQer | software resource | A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24124457 | Commercial license, Free | biotools:ceqer, OMICS_00329 | https://bio.tools/ceqer | SCR_010813 | SciCrunch Registry | Comparative Exome Quantification analyzer | 2026-09-19 12:52:00 | 7 | |||||
|
Oncodrive-fm Resource Report Resource Website 10+ mentions |
Oncodrive-fm (RRID:SCR_010781) | Oncodrive-fm | software resource | An approach to uncover driver genes or gene modules. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00157, biotools:oncodrivefm | https://bio.tools/oncodrivefm | SCR_010781 | SciCrunch Registry | 2026-09-19 12:51:59 | 15 | ||||||||
|
SSAKE Resource Report Resource Website 10+ mentions |
SSAKE (RRID:SCR_010753) | SSAKE | software resource | Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btl629 | biotools:ssake, OMICS_00033 | https://bio.tools/ssake, https://sources.debian.org/src/ssake/ | SCR_010753 | SciCrunch Registry | 2026-09-19 12:51:59 | 11 | |||||||
|
CopySeq Resource Report Resource Website 1+ mentions |
CopySeq (RRID:SCR_010758) | CopySeq | software resource | A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
PMID:21085617 | biotools:copyseq, OMICS_00055 | https://bio.tools/copyseq | SCR_010758 | SciCrunch Registry | 2026-09-19 12:51:59 | 1 | |||||||
|
FreeBayes Resource Report Resource Website 1000+ mentions |
FreeBayes (RRID:SCR_010761) | FreeBayes | software resource | A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment. | single-nucleotide polymorphism, indel, insertion, deletion, multi-nucleotide polymorphism, complex event, composite insertion, substitution event, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:arXiv:1207.3907 | OMICS_00059, biotools:freebayes | https://bio.tools/freebayes, https://sources.debian.org/src/freebayes/ | SCR_010761 | SciCrunch Registry | 2026-09-19 12:51:59 | 2118 | |||||||
|
ProDesign Resource Report Resource Website 10+ mentions |
ProDesign (RRID:SCR_010966) | ProDesign | analysis service resource, data analysis service, production service resource, service resource, software resource | Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17392329 | Licensed free of charge for academic use | OMICS_00837, biotools:prodesign | https://bio.tools/prodesign | SCR_010966 | SciCrunch Registry | 2026-09-19 12:52:03 | 19 | ||||||
|
MICSA Resource Report Resource Website |
MICSA (RRID:SCR_010860) | MICSA | software resource | A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Curie Institute; Paris; France |
biotools:micsa, OMICS_00447 | https://bio.tools/micsa | SCR_010860 | SciCrunch Registry | MICSA: Motif Identification for ChIP-Seq Analysis, Motif Identification for ChIP-Seq Analysis | 2026-09-19 12:52:01 | 0 | |||||||
|
NOrMAL Resource Report Resource Website 50+ mentions |
NOrMAL (RRID:SCR_010889) | NOrMAL | software resource | A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6 | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
Free for academic use | OMICS_00504, biotools:normal | https://bio.tools/normal | SCR_010889 | SciCrunch Registry | NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model | 2026-09-19 12:52:01 | 84 | ||||||
|
Asterias Resource Report Resource Website 1+ mentions |
Asterias (RRID:SCR_010936) | Asterias | software resource | A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:17488846 | Public | OMICS_00747, biotools:asterias | https://bio.tools/asterias | SCR_010936 | SciCrunch Registry | 2026-09-19 12:52:02 | 1 | ||||||
|
Chipster Resource Report Resource Website 50+ mentions |
Chipster (RRID:SCR_010939) | Chipster | software resource | A user-friendly analysis software for high-throughput data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00751, biotools:chipster | https://bio.tools/chipster | SCR_010939 | SciCrunch Registry | 2026-09-19 12:52:02 | 85 | ||||||||
|
PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family. | protein model, protein sequence, gene family, protein, transcriptional control, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Fond der Chemischen Industrie ; German Federal Ministry of Education and Research ; University of Potsdam ; Germany |
PMID:19858103 PMID:17286856 |
Free, Freely available | biotools:plntfdb, OMICS_00561 | http://plntfdb.bio.uni-potsdam.de/v3.0/, https://bio.tools/plntfdb | SCR_010899 | SciCrunch Registry | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-09-19 12:52:02 | 218 | |||||
|
MethMarker Resource Report Resource Website 1+ mentions |
MethMarker (RRID:SCR_010908) | MethMarker | software resource | Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser. | dna methylation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
PMID:19804638 | Acknowledgement requested | OMICS_00636, biotools:methmarker | https://bio.tools/methmarker | SCR_010908 | SciCrunch Registry | 2026-09-19 12:52:02 | 3 | ||||||
|
SISSRs Resource Report Resource Website 10+ mentions |
SISSRs (RRID:SCR_010866) | SISSRs | software resource | Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. | perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:18684996 PMID:22130889 |
biotools:sissrs, OMICS_00463 | https://bio.tools/sissrs | SCR_010866 | SciCrunch Registry | Site Identification from Short Sequence Reads | 2026-09-19 12:52:01 | 16 | ||||||
|
ZINBA Resource Report Resource Website 10+ mentions |
ZINBA (RRID:SCR_010868) | ZINBA | software resource | Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21787385 | GNU General Public License, v3 | biotools:zinba, OMICS_00465 | https://bio.tools/zinba | SCR_010868 | SciCrunch Registry | zinba - Zero Inflated Negative Binomial Algorithm, Zero Inflated Negative Binomial Algorithm | 2026-09-19 12:52:01 | 13 | |||||
|
Aroma.affymetrix Resource Report Resource Website 10+ mentions |
Aroma.affymetrix (RRID:SCR_010919) | Aroma.affymetrix | software resource | An R package for analyzing large Affymetrix data sets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00703, biotools:aroma.affymetrix | https://bio.tools/aroma.affymetrix | SCR_010919 | SciCrunch Registry | 2026-09-19 12:52:02 | 34 |
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