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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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dna-bison Resource Report Resource Website 1+ mentions |
dna-bison (RRID:SCR_005913) | dna-bison | software resource | Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00582 | SCR_005913 | 2026-08-29 11:22:27 | 1 | ||||||||||
|
COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-08-29 11:22:42 | 19 | |||||
|
GARM Resource Report Resource Website 10+ mentions |
GARM (RRID:SCR_006731) | GARM | software resource | A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01420 | SCR_006731 | Genome Assembler Reconcilation and Merging | 2026-08-29 11:22:43 | 12 | |||||||||
|
Diffusion Tensor Imaging ToolKit Resource Report Resource Website 10+ mentions |
Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) | DTI-TK | data processing software, image analysis software, software application, software resource, software toolkit | A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation | dti, visualization, segmentation, resampling, smoothing, warping, registration, spatial normalization, atlas construction, analysis, atlas application, intersubject, image-to-template, analyze, nifti-1, macos, linux |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury is related to: Camino is related to: MRI Studio has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: SourceForge |
NIBIB 1R03EB009321-01 | Free, Available for download, Freely available | nlx_153914 | http://www.nitrc.org/projects/dtitk | SCR_001642 | 2026-08-29 11:20:47 | 25 | ||||||
|
PennSeq Resource Report Resource Website 1+ mentions |
PennSeq (RRID:SCR_001763) | PennSeq | software resource | Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. | isoform, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24362841 | Free, Available for download, Freely available | biotools:pennseq, OMICS_01946 | https://bio.tools/pennseq | SCR_001763 | 2026-08-29 11:20:50 | 4 | ||||||
|
openADAM Resource Report Resource Website |
openADAM (RRID:SCR_002018) | openADAM | data management software, software application, software resource | A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms. | php, perl, front end, affymetrix genechip mapping array, affymetrix genome-wide human snp array, data management, affymetrix, snp, genome-wide association |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19117518 | Free, Available for download, Freely available | OMICS_01921 | SCR_002018 | 2026-08-29 11:21:10 | 0 | |||||||
|
DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-08-29 11:20:57 | 1 | ||||||
|
SNVer Resource Report Resource Website 50+ mentions |
SNVer (RRID:SCR_002061) | data analysis software, data processing software, software application, software resource | Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data. | statistical analysis software, sequencing, dna, whole-exome, whole-genome, variant, bio.tools |
lists: SAMTOOLS is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:21813454 | Free, Available for download, Freely available | OMICS_00076, biotools:snver | https://sourceforge.net/projects/snver/, https://bio.tools/snver | SCR_002061 | 2026-08-29 11:20:58 | 52 | |||||||
|
Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray, https://sources.debian.org/src/ray/ | SCR_001916 | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-08-29 11:21:07 | 1 | |||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | 2026-08-29 11:21:10 | 11 | |||||||
|
Matchprot Resource Report Resource Website |
Matchprot (RRID:SCR_002163) | software resource | A pairwise protein structure alignment software. | standalone software, c |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17338826 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03666 | SCR_002163 | 2026-08-29 11:21:13 | 0 | ||||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | 2026-08-29 11:22:05 | 0 | ||||||
|
CB-Commander Resource Report Resource Website |
CB-Commander (RRID:SCR_004237) | CB-Commander | software resource | A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline. | java, java swing, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
GNU General Public License, v2 | OMICS_01534 | http://sourceforge.net/projects/cb-commander/ | SCR_004237 | 2026-08-29 11:21:59 | 0 | |||||||
|
PASHA Resource Report Resource Website 10+ mentions |
PASHA (RRID:SCR_004455) | PASHA | software resource | A parallel short read assembler for large genomes using de Bruijn graphs. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21867511 | OMICS_00024 | SCR_004455 | 2026-08-29 11:22:05 | 10 | |||||||||
|
MGED Ontology Resource Report Resource Website 1+ mentions |
MGED Ontology (RRID:SCR_004484) | MO | controlled vocabulary, data or information resource, ontology | An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. | microarray, biomaterial, treatment, mage, owl |
is listed by: BioPortal is related to: MIAME is related to: MIAME is related to: RNA Abundance Database has parent organization: Functional Genomics Data Society has parent organization: SourceForge |
NIBIB ; NHGRI P41HG003619 |
PMID:16428806 | nlx_47223 | http://purl.bioontology.org/ontology/MO | SCR_004484 | Microarray and Gene Expression Data Ontology | 2026-08-29 11:22:08 | 1 | |||||
|
SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | 2026-08-29 11:22:07 | 2 | |||||||
|
LMAT Resource Report Resource Website 10+ mentions |
LMAT (RRID:SCR_004646) | LMAT | software resource | Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. | c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome |
is listed by: OMICtools has parent organization: Lawrence Livermore National Laboratory has parent organization: SourceForge |
PMID:23828782 | Open unspecified license | OMICS_02285 | SCR_004646 | Livermore Metagenomics Analysis Toolkit | 2026-08-29 11:22:09 | 15 | ||||||
|
USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-08-29 11:21:59 | 131 | ||||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-08-29 11:22:13 | 19 | ||||||
|
SobekCM Resource Report Resource Website |
SobekCM (RRID:SCR_003225) | SobekCM | software resource | Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories. | archiving, resource management, metadata standard, ontology, data repository, research object, c#, windows |
is listed by: FORCE11 has parent organization: University of Florida; Florida; USA has parent organization: Google Code has parent organization: SourceForge |
NEH ; NSF ; NHPRC ; IMLS |
Free, Available for download, Freely available | nlx_157266 | SCR_003225 | SobekCM Digital Repository Software, SobekCM : Digital Content Management System, SobekCM Digital Repository | 2026-08-29 11:21:47 | 0 |
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