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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CPFP Resource Report Resource Website 1+ mentions |
CPFP (RRID:SCR_012043) | data analysis software, data processing software, software application, software resource | Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:20189941 | OMICS_02448, biotools:cpfp | https://bio.tools/cpfp | SCR_012043 | SciCrunch Registry | Central Proteomics Facilities Pipeline | 2026-10-17 01:28:28 | 7 | |||||||
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | SciCrunch Registry | 2026-10-17 01:28:28 | 0 | ||||||||
|
easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | SciCrunch Registry | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-10-17 01:28:37 | 30 | |||||
|
VisSR Resource Report Resource Website 1+ mentions |
VisSR (RRID:SCR_012024) | VisSR | data processing software, data visualization software, software application, software resource | Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat. |
is listed by: OMICtools is listed by: UEA sRNA Workbench is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
OMICS_02107, biotools:vissr | https://bio.tools/vissr | SCR_012024 | SciCrunch Registry | Visualisation of sRNAs | 2026-10-17 01:27:52 | 3 | ||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | SciCrunch Registry | Network Analysis and Inference Library | 2026-10-17 01:28:17 | 8 | ||||||
|
LocalAli Resource Report Resource Website 1+ mentions |
LocalAli (RRID:SCR_012147) | software resource | A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:25282642 | GNU General Public License | biotools:localali, OMICS_06337 | https://bio.tools/localali | SCR_012147 | SciCrunch Registry | 2026-10-17 01:28:17 | 1 | |||||||
|
Isaac Resource Report Resource Website 50+ mentions |
Isaac (RRID:SCR_012772) | Isaac | software resource | Whole genome secondary analysis on Illumina sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:isaac, OMICS_00289 | https://bio.tools/isaac | SCR_012772 | SciCrunch Registry | 2026-10-17 01:28:29 | 74 | ||||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, source code, web service | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | SciCrunch Registry | Sorting Intolerant From Tolerant | 2026-10-17 01:28:06 | 10996 | |||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | SciCrunch Registry | 2026-10-17 01:28:05 | 319 | ||||||||
|
Ngs backbone Resource Report Resource Website 1+ mentions |
Ngs backbone (RRID:SCR_012907) | Ngs_backbone | software resource | A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:ngs_backbone, OMICS_01132 | https://bio.tools/ngs_backbone | SCR_012907 | SciCrunch Registry | 2026-10-17 01:28:09 | 1 | ||||||||
|
rqubic Resource Report Resource Website |
rqubic (RRID:SCR_012869) | rqubic | software resource | This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19509312 | Free | biotools:rqubic, OMICS_01799 | https://bio.tools/rqubic | SCR_012869 | SciCrunch Registry | rqubic - Qualitative biclustering algorithm for expression data analysis in R | 2026-10-17 01:28:44 | 0 | |||||
|
DiffBind Resource Report Resource Website 1000+ mentions |
DiffBind (RRID:SCR_012918) | DiffBind | software resource | Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
biotools:diffbind, OMICS_00471 | https://bio.tools/diffbind | SCR_012918 | SciCrunch Registry | Differential Binding Analysis of ChIP-Seq peak data | 2026-10-17 01:28:34 | 1449 | |||||||
|
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 | 2026-10-17 01:28:38 | 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 | 2026-10-17 01:28:09 | 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 | 2026-10-17 01:28:33 | 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 | 2026-10-17 01:28:34 | 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 | 2026-10-17 01:28:46 | 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 | 2026-10-17 01:28:47 | 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 | 2026-10-17 01:28:36 | 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 | 2026-10-17 01:28:36 | 83 |
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