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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-07-25 12:07:02 | 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 | Comparative Exome Quantification analyzer | 2026-07-25 12:07:07 | 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 | 2026-07-25 12:07:06 | 14 | ||||||||
|
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 | 2026-07-25 12:07:02 | 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 | 2026-07-25 12:07:06 | 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 | 2026-07-25 12:07:06 | 1982 | |||||||
|
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 | MICSA: Motif Identification for ChIP-Seq Analysis, Motif Identification for ChIP-Seq Analysis | 2026-07-25 12:07:06 | 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 | NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model | 2026-07-25 12:07:06 | 83 | ||||||
|
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 | 2026-07-25 12:07:05 | 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 | 2026-07-25 12:07:05 | 81 | ||||||||
|
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 | 2026-07-25 12:07:09 | 2 | ||||||
|
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 | Site Identification from Short Sequence Reads | 2026-07-25 12:07:06 | 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 | zinba - Zero Inflated Negative Binomial Algorithm, Zero Inflated Negative Binomial Algorithm | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:05 | 32 | ||||||||
|
NURD Resource Report Resource Website 50+ mentions |
NURD (RRID:SCR_010988) | NURD | software resource | An algorithm to inference isoform expression., 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 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nurd, OMICS_01283 | https://bio.tools/nurd | SCR_010988 | 2026-07-25 12:07:08 | 72 | |||||||
|
cutadapt Resource Report Resource Website 5000+ mentions |
cutadapt (RRID:SCR_011841) | cutadapt | software resource | Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is required by: SL-quant works with: Trim Galore |
DOI:10.14806/ej.17.1.200 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01086, biotools:cutadapt | https://bio.tools/cutadapt | https://sources.debian.org/src/cutadapt/ | SCR_011841 | 2026-07-25 12:07:21 | 7023 | |||||
|
SynTView Resource Report Resource Website 1+ mentions |
SynTView (RRID:SCR_011939) | SynTView | software resource | An interactive multi-view genome browser for next-generation comparative microorganism genomics. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01500, biotools:syntview | https://bio.tools/syntview | SCR_011939 | 2026-07-25 12:07:23 | 7 | ||||||||
|
NeSSM Resource Report Resource Website 10+ mentions |
NeSSM (RRID:SCR_011941) | NeSSM | software resource | A Next-Generation Sequencing Simulator for Metagenomics. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01510, biotools:nessm | https://bio.tools/nessm | SCR_011941 | 2026-07-25 12:07:27 | 11 | ||||||||
|
MetaVelvet Resource Report Resource Website 50+ mentions |
MetaVelvet (RRID:SCR_011915) | MetaVelvet | software resource | Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01427, biotools:metavelvet | https://bio.tools/metavelvet | SCR_011915 | MetaVelvet: a short read assember for metagenomics | 2026-07-25 12:07:23 | 78 | |||||||
|
GeneStitch Resource Report Resource Website |
GeneStitch (RRID:SCR_011910) | GeneStitch | software resource | Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes. | gene fragment, network matching, gene assembly, metagenomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Indiana University; Indiana; USA |
PMID:22962453 | Open unspecified license | OMICS_01421, biotools:genestitch | https://bio.tools/genestitch | SCR_011910 | GeneStitch: Network Matching Algorithm to Gene Assembly | 2026-07-25 12:07:24 | 0 |
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