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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | software application, data analysis software, sequence analysis software, software resource, data processing software, standalone software | Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments. | resequencing analysis, exome variant detection, pipeline, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
BLUEPRINT Consortium FP7/2007-2013 282510; Spanish Ministry of Economy and Competitiveness BIO2007-666855 |
PMID:23630175 | Free, Available for download | biotools:rubioseq, OMICS_00072 | https://sourceforge.net/projects/rubioseq/files/, https://bio.tools/rubioseq | SCR_002508 | RUbioSeq+ | 2026-07-28 09:40:37 | 12 | |||||
|
Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | software resource, data access protocol, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-07-28 09:39:57 | 16 | |||||
|
CovalentDock Cloud Resource Report Resource Website |
CovalentDock Cloud (RRID:SCR_000126) | CovalentDock Cloud | software resource, data access protocol, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor. | protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23034731 | THIS RESOURCE IS NO LONGER IN SERVICE | covalentdock_cloud, OMICS_01597 | https://bio.tools/covalentdock_cloud | SCR_000126 | 2026-07-28 09:39:57 | 0 | ||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | software application, data analysis software, software resource, data processing software, software toolkit | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | cn.farms - factor analysis for copy number estimation | 2026-07-28 09:39:57 | 0 | |||||
|
Dipy Resource Report Resource Website 10+ mentions |
Dipy (RRID:SCR_000029) | DIPY | software application, data analysis software, software resource, data processing software, software toolkit | Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data. | MRI, magnetic resonance, diffusion data analysis, diffusion MRI data, diffusion MRI data analysis, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Neuroimaging in Python has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:24600385 | Free, Available for download, Freely available | nlx_155745 | https://sources.debian.org/src/python-dipy/, http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web, | http://nipy.org/dipy/ | SCR_000029 | Diffusion Imaging In Python, NIPY Diffusion Imaging Analysis | 2026-07-28 09:39:54 | 15 | ||||
|
PyMOL Resource Report Resource Website 1000+ mentions |
PyMOL (RRID:SCR_000305) | software application, software resource, data processing software, data visualization software, 3d visualization software | A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures. | visualization, molecule, 3d, molecular structure visualization, molecular visualization system, |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Restricted | nlx_156834, OMICS_03802 | https://sources.debian.org/src/pymol/ | SCR_000305 | 2026-07-28 09:39:58 | 3422 | ||||||||
|
Fusion Analyser Resource Report Resource Website |
Fusion Analyser (RRID:SCR_000059) | software application, software resource, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data. | gene fusion, rna-seq, paired-end rna-seq data, fusion event, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22570408 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01347, biotools:fusionanalyser | https://bio.tools/fusionanalyser | SCR_000059 | FusionAnalyser | 2026-07-28 09:39:55 | 0 | ||||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | software application, data analysis software, sequence analysis software, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | CorMut - Detect the correlated mutations based on selection pressure | 2026-07-28 09:39:55 | 0 | ||||||
|
Bio-Formats Resource Report Resource Website 50+ mentions |
Bio-Formats (RRID:SCR_000450) | Bio-Formats | software application, software resource, software library, standalone software, software toolkit | Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. | Java library, reading microscopy image data files, writing image data, standardized format, open format, |
is listed by: FORCE11 is listed by: Debian is related to: OMERO is related to: OME-TIFF Format has parent organization: OME - Open Microscopy Environment |
Wellcome Trust | Free, Available for download, Freely available | nif-0000-30175 | http://www.force11.org/node/4810, http://www.loci.wisc.edu/software/bio-formats, https://sources.debian.org/src/libbio-formats-java/ | SCR_000450 | , BioFormats, Bio-Formats Library, The Bio-Formats Library | 2026-07-28 09:40:00 | 60 | |||||
|
RNAcontext Resource Report Resource Website 1+ mentions |
RNAcontext (RRID:SCR_000179) | RNAcontext | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website. | rna-binding protein, motif, rna sequence, rna structure, rna, binding preference, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
PMID:20617199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02253, biotools:rnacontext | https://bio.tools/rnacontext | SCR_000179 | 2026-07-28 09:39:56 | 2 | ||||||
|
pbcore Resource Report Resource Website |
pbcore (RRID:SCR_000454) | software library, software toolkit, software resource | Software Python library for reading and writing PacBio data files. | software package, python |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | OMICS_05135 | http://pacificbiosciences.github.io/pbcore/, https://sources.debian.org/src/python3-pbcore/ | SCR_000454 | 2026-07-28 09:39:59 | 0 | ||||||||
|
nmrML Resource Report Resource Website 1+ mentions |
nmrML (RRID:SCR_000467) | nmrML | narrative resource, markup language, data or information resource, standard specification, interchange format | An open mark-up language for NMR data. | nuclear magnetic resonance, bio.tools |
is listed by: bio.tools is listed by: Debian is parent organization of: nmrCV |
nlx_157309, biotools:nmrml_converter | https://bio.tools/nmrml_converter | SCR_000467 | 2026-07-28 09:40:00 | 9 | ||||||||
|
OpenElectrophy Resource Report Resource Website 10+ mentions |
OpenElectrophy (RRID:SCR_000819) | OpenElectrophy | software application, software resource, data analysis software, data processing software | Software Python module for electrophysiology data analysis. | neurophysiology, electrophysiology, python, intracellular, extracellular, data sharing, analysis sharing, neural signal, spike, oscillation, mysql, eeg, meg, electrocorticography |
uses: Neo is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: NeuralEnsemble |
NIBIB 5R24EB029173 | PMID:19521545 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151873 | http://www.nitrc.org/projects/openelectrophy, https://sources.debian.org/src/openelectrophy/ | SCR_000819 | 2026-07-28 09:40:08 | 10 | |||||
|
pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | software application, software resource, data analysis software, data processing software | Software for adaptive Gene Picking for Microarray Expression Data Analysis. | microarray, gene expression, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02007, biotools:pickgene | https://bio.tools/pickgene | SCR_001331 | 2026-07-28 09:40:10 | 0 | |||||||
|
VCFtools Resource Report Resource Website 1000+ mentions |
VCFtools (RRID:SCR_001235) | software application, software resource, data management software | Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API. | perl, genetic variation, variant call format, software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21653522 DOI:10.1093/bioinformatics/btr330 |
Free, Available for download, Freely available | OMICS_02105, biotools:vcftools, SCR_012092, OMICS_05112 | https://bio.tools/vcftools, https://sources.debian.org/src/vcftools/ | http://vcftools.sourceforge.net/ | SCR_001235 | Variant Call Format Tools | 2026-07-28 09:40:09 | 4095 | |||||
|
ShortFuse Resource Report Resource Website 1+ mentions |
ShortFuse (RRID:SCR_001107) | software application, data analysis software, sequence analysis software, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2. | fusion transcripts, rna, sequence data, python 2, c++, sequence analysis software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21330288 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:shortfuse, OMICS_01355 | https://bio.tools/shortfuse | SCR_001107 | 2026-07-28 09:40:08 | 1 | |||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | software application, software resource, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-07-28 09:40:13 | 0 | |||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | software application, data analysis software, sequence analysis software, software resource, data processing software | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-07-28 09:40:09 | 30 | ||||||
|
DSRC Resource Report Resource Website 1+ mentions |
DSRC (RRID:SCR_001005) | DSRC | software application, software resource, data management software | An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression. | fastq, dna sequence, compression, multithread, data management software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21252073 | Free, Available as binary, Available as source code | biotools:dsrc, OMICS_00955 | https://bio.tools/dsrc | SCR_001005 | DNA Sequence Reads Compression, DNA Sequence Reads Compression (DSRC) | 2026-07-28 09:40:09 | 1 | |||||
|
Illuminator Resource Report Resource Website |
Illuminator (RRID:SCR_001019) | software application, data analysis software, sequence analysis software, software resource, data processing software | A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels. | sequence analysis software, sequence alignment, software, mutation detection, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:21621601 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:illuminator, OMICS_02165 | https://bio.tools/illuminator | SCR_001019 | 2026-07-28 09:40:10 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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