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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
eisa Resource Report Resource Website 1+ mentions |
eisa (RRID:SCR_012883) | eisa | software resource | A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free | OMICS_01801, biotools:eisa | https://bio.tools/eisa | SCR_012883 | SciCrunch Registry | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-10-10 12:38:54 | 2 | ||||||
|
GeneProf Resource Report Resource Website 10+ mentions |
GeneProf (RRID:SCR_012927) | GeneProf | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally. | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Edinburgh; Scotland; United Kingdom |
MRC ; European Union Framework 7 Project EuroSyStem |
PMID:22205509 PMID:24174536 |
Acknowledgement requested | biotools:geneprof, OMICS_00442 | https://bio.tools/geneprof | SCR_012927 | SciCrunch Registry | 2026-10-10 12:38:58 | 15 | |||||
|
Trowel Resource Report Resource Website 1+ mentions |
Trowel (RRID:SCR_012890) | Trowel | software resource | An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. | c++, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Apache License | OMICS_01111, biotools:trowel | https://bio.tools/trowel/ | SCR_012890 | SciCrunch Registry | Trowel - Error Correction Module for Illumina Sequencing Reads, Trowel - Sequencing Error Corrector | 2026-10-10 12:39:09 | 5 | ||||||
|
CSAR Resource Report Resource Website 50+ mentions |
CSAR (RRID:SCR_012930) | CSAR | software resource | Statistical tools for the analysis of ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21554688 | Free | OMICS_00435, biotools:csar | https://bio.tools/csar | SCR_012930 | SciCrunch Registry | 2026-10-10 12:39:09 | 50 | ||||||
|
SeqPrep Resource Report Resource Website 1000+ mentions |
SeqPrep (RRID:SCR_013004) | SeqPrep | software resource | A program to merge paired end Illumina reads that are overlapping into a single longer read. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
biotools:seqprep, OMICS_01092 | https://bio.tools/seqprep, https://sources.debian.org/src/seqprep/ | SCR_013004 | SciCrunch Registry | SeqPrep - Tool for stripping adaptors and/or merging paired reads with overlap into single reads | 2026-10-10 12:39:19 | 1146 | |||||||
|
phyloseq Resource Report Resource Website 1000+ mentions |
phyloseq (RRID:SCR_013080) | phyloseq | software resource | Software for handling and analysis of high-throughput microbiome census data. | bio.tools |
is used by: microViz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1371/journal.pone.0061217 | OMICS_01520, biotools:phyloseq | https://bio.tools/phyloseq, https://sources.debian.org/src/r-bioc-phyloseq/ | SCR_013080 | SciCrunch Registry | 2026-10-10 12:39:21 | 3080 | |||||||
|
PhyloPhlAn Resource Report Resource Website 100+ mentions |
PhyloPhlAn (RRID:SCR_013082) | PhyloPhlAn | software resource | Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic tree, whole-genome sequence, genome, protein |
is listed by: OMICtools is listed by: Debian has parent organization: Harvard T.H. Chan School of Public Health |
PMID:23942190 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01525 | https://sources.debian.org/src/phylophlan/ | SCR_013082 | SciCrunch Registry | PhyloPhlAn: microbial Tree of Life using 400 universal proteins | 2026-10-10 12:39:11 | 340 | |||||
|
QuantiSNP Resource Report Resource Website 50+ mentions |
QuantiSNP (RRID:SCR_013091) | QuantiSNP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development. | matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17341461 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:quantisnp, OMICS_00730 | https://bio.tools/quantisnp | SCR_013091 | SciCrunch Registry | 2026-10-10 12:39:11 | 83 | ||||||
|
AMOS Resource Report Resource Website 1000+ mentions |
AMOS (RRID:SCR_013067) | AMOS | software resource | A collection of tools and class interfaces for the assembly of DNA reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1093/bib/bbr074 | OMICS_00008, biotools:amos | https://bio.tools/amos, https://sources.debian.org/src/ampliconnoise/ | SCR_013067 | SciCrunch Registry | 2026-10-10 12:39:11 | 4855 | |||||||
|
Reptile Resource Report Resource Website 10+ mentions |
Reptile (RRID:SCR_013075) | Reptile | software resource | A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20834037 | biotools:reptile, OMICS_01109 | https://bio.tools/reptile | SCR_013075 | SciCrunch Registry | 2026-10-10 12:39:11 | 30 | |||||||
|
IUPHAR/BPS Guide to Pharmacology Resource Report Resource Website 1000+ mentions |
IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) | IUPHAR Database, IUPHAR-DB, IUPHAR GPCR, IUPHAR RECEPTOR | data or information resource, database, narrative resource, portal, standard specification | Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. | pharmacology, drug discovery, portal, guide, physiology, molecular structure, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: NC-IUPHAR |
Wellcome Trust | PMID:21087994 | nif-0000-03056, biotools:iuphar-db, r3d100013308 | https://bio.tools/iuphar-db, https://doi.org/10.17616/R31NJMRG | http://www.iuphar-db.org | SCR_013077 | SciCrunch Registry | International Union of Pharmacology Database, International Union of Basic and Clinical Pharmacology Database | 2026-10-10 12:38:58 | 2375 | ||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | SciCrunch Registry | 2026-10-10 12:39:25 | 320 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | SciCrunch Registry | Telescoper - De novo assembly algorithm | 2026-10-10 12:39:12 | 0 | ||||||
|
IsoLasso Resource Report Resource Website 1+ mentions |
IsoLasso (RRID:SCR_013176) | IsoLasso | 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 |
OMICS_01320, biotools:isolasso | https://bio.tools/isolasso | SCR_013176 | SciCrunch Registry | 2026-10-10 12:38:59 | 3 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | SciCrunch Registry | heurAA - NGS multiplexed amplicon aligner | 2026-10-10 12:39:12 | 0 | ||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | SciCrunch Registry | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-10-10 12:39:25 | 1418 | ||||
|
MAP Resource Report Resource Website 1+ mentions |
MAP (RRID:SCR_013216) | software resource | This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., 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 has parent organization: Peking University; Beijing; China |
PMID:22495746 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01424, biotools:MAP | https://bio.tools/MAP | SCR_013216 | SciCrunch Registry | Metagenomic Assembly Program | 2026-10-10 12:39:23 | 1 | ||||||
|
PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | data analysis software, data processing software, simulation software, software application, software resource | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | SciCrunch Registry | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-10-10 12:39:23 | 4723 | |||||
|
Crossbow Resource Report Resource Website 1+ mentions |
Crossbow (RRID:SCR_013306) | Crossbow | software resource | A scalable software pipeline for whole genome resequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19930550 DOI:10.1186/gb-2009-10-11-r134 |
biotools:crossbow, OMICS_00284 | https://bio.tools/crossbow | https://sources.debian.org/src/crossbow/ | SCR_013306 | SciCrunch Registry | 2026-10-10 12:39:26 | 5 | ||||||
|
INCLUSive Resource Report Resource Website 1+ mentions |
INCLUSive (RRID:SCR_013488) | INCLUSive | software resource | A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:12824346 | Acknowledgement requested | OMICS_00766, biotools:inclusive | https://bio.tools/inclusive | SCR_013488 | SciCrunch Registry | 2026-10-10 12:39:08 | 7 |
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