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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PRICE Resource Report Resource Website 100+ mentions |
PRICE (RRID:SCR_013063) | PRICE | software resource | Software for a de novo genome assembler implemented in C++. | c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
OMICS_01430, biotools:price | https://bio.tools/price | SCR_013063 | SciCrunch Registry | Paired-Read Iterative Contig Extension | 2026-10-24 12:46:59 | 165 | |||||||
|
OntoQuest Resource Report Resource Website |
OntoQuest (RRID:SCR_013281) | OntoQuest | software resource | An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework. | ontology, interoperability, owl, middleware, web service, bio.tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: NIFSTD is related to: NIF Web Services has parent organization: Neuroscience Information Framework |
PMID:18958629 | biotools:list_ontologies, biotools:ontoquest_ws, nlx_151737 | https://bio.tools/list_ontologies, https://bio.tools/ontoquest_ws | SCR_013281 | SciCrunch Registry | Ontoquest | 2026-10-24 12:47:02 | 0 | ||||||
|
chimerascan Resource Report Resource Website 50+ mentions |
chimerascan (RRID:SCR_013298) | chimerascan | software resource | Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data. | Gene fusion detection, paired-end RNA sequencing data, RNA sequencing data, chimeric transcripts detection, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:chimerascan, OMICS_01343 | https://bio.tools/chimerascan | SCR_013298 | SciCrunch Registry | 2026-10-24 12:47:03 | 53 | |||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | SciCrunch Registry | 2026-10-24 12:47:03 | 7 | ||||||||
|
GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | SciCrunch Registry | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-10-24 12:47:03 | 24 | ||||
|
PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | SciCrunch Registry | Plant Natural Antisense Transcripts DataBase | 2026-10-24 12:47:02 | 9 | ||||
|
CEM Resource Report Resource Website 1+ mentions |
CEM (RRID:SCR_013241) | CEM | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | 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 |
OMICS_01271, biotools:cem | https://bio.tools/cem | SCR_013241 | SciCrunch Registry | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | 2026-10-24 12:47:02 | 1 | |||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | SciCrunch Registry | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-10-24 12:47:01 | 38 | ||||||
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Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | SciCrunch Registry | 2026-10-24 12:47:04 | 72 | ||||||||
|
Dali Server Resource Report Resource Website 500+ mentions |
Dali Server (RRID:SCR_013433) | analysis service resource, data analysis service, production service resource, service resource, software resource | Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use. | Protein structure comparison server, protein structure, comparison server, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:20457744 | Free, Freely available | biotools:dali | https://bio.tools/dali | SCR_013433 | SciCrunch Registry | Dali | 2026-10-24 12:47:04 | 534 | ||||||
|
ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | data analysis software, data processing software, software application, software resource | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | SciCrunch Registry | 2026-10-24 12:47:03 | 133 | ||||||||
|
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers Resource Report Resource Website 1+ mentions |
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) | PCS | software resource | A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs. | perl, perl script, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
biotools:pcs, nlx_33020 | https://bio.tools/pcs | http://bioinfo.au.tsinghua.edu.cn/member/~gujin/pcs/ | SCR_013409 | SciCrunch Registry | Pairwise Conservation Scores | 2026-10-24 12:47:03 | 3 | ||||||
|
CNV-seq Resource Report Resource Website 100+ mentions |
CNV-seq (RRID:SCR_013357) | CNV-seq | software resource | A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., 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:cnv-seq, OMICS_00339 | https://bio.tools/cnv-seq | SCR_013357 | SciCrunch Registry | 2026-10-24 12:47:03 | 167 | |||||||
|
PASA Resource Report Resource Website 1000+ mentions |
PASA (RRID:SCR_014656) | data analysis software, data processing software, sequence analysis software, software application, software resource | Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute. | gene structure, annotation, gene structure analysis tool, spliced alignment, transcript sequence, bio.tools |
is used by: BRO_annotation is listed by: Debian is listed by: bio.tools |
DOI:10.1093/nar/gkg770 | Available for download | biotools:PASA | https://bio.tools/PASA | SCR_014656 | SciCrunch Registry | Program to Assemble Spliced Alignments (PASA), Program to Assemble Spliced Alignments | 2026-10-24 12:49:11 | 1123 | ||||||
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Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | data processing software, software application, software resource, workflow software | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/, https://bio.tools/ambergpumdsimulation | SCR_014389 | SciCrunch Registry | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-10-24 12:49:11 | 1 | ||||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software resource, software toolkit | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | SciCrunch Registry | 2026-10-24 12:49:10 | 77 | ||||||||
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HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | data processing software, software application, software resource, workflow software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
ABS4NGS project ; ERC Advanced Investigator award ; European Commission ; European Research Coucil ; France Genomique National infrastructure ; Howard Hughes Medical Institute ; Labex Deep ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | SciCrunch Registry | 2026-10-24 12:49:14 | 238 | ||||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, data processing software, software application, software resource | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | SciCrunch Registry | OrthoFinder2, OrthoFinder | 2026-10-24 12:49:14 | 3413 | |||||
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tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data analysis software, data processing software, software application, software resource | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
European Commission ; NCI T32 CA009337; SNSF 143883 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | SciCrunch Registry | tximport v1.4.0 | 2026-10-24 12:49:13 | 100 | ||||
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Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele, https://bio.tools/nephele | SCR_016595 | SciCrunch Registry | 2026-10-24 12:49:13 | 36 |
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