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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | software application, data analytics software, software resource | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | QmRLFS finder | 2026-08-06 09:28:23 | 13 | |||||
|
FunRich: Functional Enrichment analysis tool Resource Report Resource Website 100+ mentions |
FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) | standalone software, software application, data analytics software, software resource | A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts. | network analysis, background database, charts, data analytics software, standalone software, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:25921073 PMID:26149235 |
Public, Open Source | biotools:funrich | https://bio.tools/funrich | SCR_014467 | 2026-08-06 09:28:21 | 338 | |||||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | software application, data analytics software, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-08-06 09:28:59 | 1239 | ||||||
|
Myriads Resource Report Resource Website 1+ mentions |
Myriads (RRID:SCR_017447) | software application, data analytics software, software resource | Software package for p value based multiple testing that also implements dependence test and p-value simulation. | P value, multiple, testing, simulation, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: bio.tools is listed by: Debian |
NIMH MH111416 | PMID:29186285 | biotools:myriads | https://bio.tools/myriads | SCR_017447 | SGoF+ | 2026-08-06 09:29:04 | 1 | ||||||
|
PyRosetta Resource Report Resource Website 10+ mentions |
PyRosetta (RRID:SCR_018541) | standalone software, software application, software resource | Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions. | Molecular modeling, custom structure prediction, design algorithm, energy function, scoring function, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian is related to: Rosetta has parent organization: Johns Hopkins University; Maryland; USA |
NIGMS R01 GM73151; NIGMS R01 GM078221; NSF 0846324 |
PMID:20061306 | Free, Freely available | biotools:pyrosetta | https://bio.tools/pyrosetta | SCR_018541 | Python Rosetta | 2026-08-06 09:29:20 | 20 | |||||
|
Segway - a way to segment the genome Resource Report Resource Website 1+ mentions |
Segway - a way to segment the genome (RRID:SCR_004206) | source code, software resource | The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind. | genome annotation, source code, bayesian network model, bayesian, chip seq, dbn, bio.tools |
is used by: ENCODE is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA has parent organization: University of Toronto; Ontario; Canada |
PMID:22426492 | Free | nlx_22911, biotools:segway | https://www.pmgenomics.ca/hoffmanlab/proj/segway/, https://bitbucket.org/hoffmanlab/segway/, https://bio.tools/segway | http://noble.gs.washington.edu/proj/segway/ | SCR_004206 | Segway | 2026-08-06 09:26:03 | 8 | |||||
|
Biopieces Resource Report Resource Website 10+ mentions |
Biopieces (RRID:SCR_005783) | Biopieces | source code, software toolkit, software resource | A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014). | bioinformatics, tool, framework, biopieces, language independent, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Project Hosting |
Danish Agency for Science Technology and Innovation 272-06-0325 | GNU General Public License, v2 | nlx_149253, biotools:biopieces, OMICS_01036 | http://code.google.com/p/biopieces/, https://bio.tools/biopieces | SCR_005783 | www.biopieces.org, biopieces - Biopieces is a bioinformatic framework of tools easily used and easily created | 2026-08-06 09:26:24 | 40 | |||||
|
VIDA Resource Report Resource Website 100+ mentions |
VIDA (RRID:SCR_007111) | VIDA | data set, data or information resource | VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, users can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures. * Search homologous protein families from particular virus families * Links to complete genome sequence: Arteriviridae, Coronaviridae, Herpesviridae, Poxviridae The Virus Database at University College London has been developed as a system to organize animal virus open reading frame sequences. All known and predicted protein sequences from complete and partial genomes of particular virus families are extracted from GenBank and filtered to remove 100% redundancy. On the basis of sequence similarity the sequences are then clustered into homologous protein families (HPFs). The families are enriched with annotations including function and functional classification, related protein structures, taxonomy, length of the proteins, boundaries of the conserved region/s, virus-specific gene name and links to EMBL entries and SWISSPROT., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomics, non-vertebrate, viral genome, homologous protein, hpf, viral genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
BBSRC ; MRC |
PMID:11125070 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03628, biotools:vida | https://bio.tools/vida | http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html | SCR_007111 | Virus Database at University College London, Virus Database, VIDA Virus Database | 2026-08-06 09:26:45 | 193 | |||
|
FusionHunter Resource Report Resource Website 1+ mentions |
FusionHunter (RRID:SCR_011895) | FusionHunter | source code, software resource | Software for identifying fusion transcripts using paired-end RNA-seq. | perl, annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01350, biotools:fusionhunter | https://bio.tools/fusionhunter | SCR_011895 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-08-06 09:27:51 | 8 | |||||||
|
CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | source code, software resource | CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-08-06 09:27:17 | 5 | |||||
|
ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | software resource, data analysis software, data processing software, data visualization software, software application | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | Reactome Pathway Analysis | 2026-08-06 09:29:31 | 76 | ||||||
|
ImJoy Resource Report Resource Website 1+ mentions |
ImJoy (RRID:SCR_020935) | data analysis software, software application, software resource, data processing software | Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers. | Deep learning, flexible plugin system, deploying deep learning applications, advanced image analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download,Freely available | biotools:ImJoy | https://github.com/imjoy-team/ImJoy, https://bio.tools/ImJoy | SCR_020935 | 2026-08-06 09:29:33 | 3 | ||||||||
|
UEA sRNA Workbench Resource Report Resource Website 1+ mentions |
UEA sRNA Workbench (RRID:SCR_020947) | data analysis software, software application, software resource, data processing software | Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals. | Analysing small RNA data, analyzing miRNAs, profiling small RNA expression patterns, genetic data, bio.tools, bio.tools, bio.tools |
lists: VisSR is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/L021269/1 | PMID:29722807 | Free, Available for download, Freely available | biotools:siloco, biotools:mircat | https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench, https://bio.tools/mircat, https://bio.tools/siloco, | SCR_020947 | UEA small RNA Workbench | 2026-08-06 09:29:33 | 7 | |||||
|
PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | software resource, data analysis software, software toolkit, data processing software, software application | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-08-06 09:29:38 | 8 | ||||||
|
vcflib Resource Report Resource Website 100+ mentions |
vcflib (RRID:SCR_001231) | vcflib | software library, software toolkit, software resource | A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. | c++, sequence variation, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:vcflib, OMICS_02112 | https://bio.tools/vcflib, https://sources.debian.org/src/libvcflib-dev/ | https://sources.debian.org/src/libvcflib-dev/ | SCR_001231 | 2026-08-06 09:25:21 | 119 | ||||||
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CSDeconv Resource Report Resource Website |
CSDeconv (RRID:SCR_000016) | CSDeconv | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach. | sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription binding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Rutgers University; New Jersey; USA has parent organization: University of South Australia; Adelaide; Australia |
PMID:20028542 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00436, biotools:csdeconv | https://bio.tools/csdeconv | SCR_000016 | 2026-08-06 09:25:06 | 0 | ||||||
|
fastqz Resource Report Resource Website |
fastqz (RRID:SCR_001006) | data management software, source code, software application, software resource | Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output. | compress, source code, fastq output, fastq dna, fastq sequencing, fastq compress, fastq compressor, fastq files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00956, biotools:fastqz | https://bio.tools/fastqz | SCR_001006 | 2026-08-06 09:25:19 | 0 | |||||||
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Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | software resource, image analysis software, alignment software, data analysis software, data processing software, software application | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-08-06 09:28:59 | 188 | ||||||
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scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, software application, software resource, data processing software | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-08-06 09:28:56 | 92 | ||||
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ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data analysis software, software application, software resource, data processing software | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; Thomas G. Labrecque Foundation ; NCI U24 CA126554 |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-08-06 09:28:56 | 160 |
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