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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
NHGRI U54 HG002750; Wellcome Trust |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ | http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-09-12 12:55:36 | 33299 | |||
|
flowQB Resource Report Resource Website |
flowQB (RRID:SCR_002144) | software resource | A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05610 | http://www.bioconductor.org/packages/release/bioc/html/flowQB.html | SCR_002144 | B and CVinstrinsic calculations, flowQB - Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q | 2026-09-12 12:55:37 | 0 | |||||||
|
AmiGO Resource Report Resource Website 1000+ mentions |
AmiGO (RRID:SCR_002143) | AmiGO | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium. | search, sort, analyze, visualize, data, ontology, gene, annotation, FASEB list |
uses: GOlr is used by: NIF Data Federation is listed by: OMICtools is listed by: Gene Ontology Tools is related to: ASAP is related to: Candida Genome Database is related to: Berkeley Bioinformatics Open-Source Projects is related to: ECO is related to: Zebrafish Information Network (ZFIN) is related to: Gramene is related to: WormBase is related to: NCBI Protein Database is related to: UniProtKB is related to: GeneDB Lmajor is related to: TAIR is related to: SGD is related to: GeneDB Tbrucei is related to: VMD is related to: JCVI CMR is related to: go-db-perl is related to: Mouse Genome Informatics (MGI) is related to: NCBI is related to: FlyBase is related to: GeneDB Pfalciparum is related to: PomBase is related to: Pseudomonas Genome Database is related to: Dictyostelium discoideum genome database is related to: Plant Ontology is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: MeGO is related to: ASPGD is related to: EcoCyc is related to: Reactome is related to: SGN is related to: GO-Module is related to: Songbird Brain Transcriptome Database is related to: Rat Genome Database (RGD) is related to: RamiGO has parent organization: Gene Ontology |
NHGRI P41 HG002273 | PMID:19033274 | Free, Available for download, Freely available | OMICS_02266, nif-0000-20935 | http://sourceforge.net/projects/geneontology/ | SCR_002143 | GO Consortium, AmiGO, AmiGO 2, AmiGene Ontology, Gene Ontology Database, Gene Ontology Consortium, GO Database, The Gene Ontology Consortium | 2026-09-12 12:55:37 | 1285 | ||||
|
Cinteny Resource Report Resource Website 10+ mentions |
Cinteny (RRID:SCR_002147) | data or information resource, database, software resource, web application | Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure. | syntenic genes, genome rearrangement, online genome database | is listed by: OMICtools | NIAID R21 AI055338; NIAMS R01 AR050688 |
PMID:17343765 | Free, Freely available | OMICS_00931 | SCR_002147 | Cinteny Server for Synteny Identification and Analysis of Genome Rearrangement | 2026-09-12 12:55:37 | 18 | ||||||
|
miso-lims Resource Report Resource Website 10+ mentions |
miso-lims (RRID:SCR_002259) | MISO | software resource | Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres. | laboratory information management system, ngs sequencing, lims | is listed by: OMICtools | Open Source, Free | OMICS_01007 | SCR_002259 | MISO: An open-source LIMS for NGS sequencing centres, MISO: An open source LIMS for small-to-large scale sequencing centres | 2026-09-12 12:55:38 | 20 | |||||||
|
flowFit Resource Report Resource Website 1+ mentions |
flowFit (RRID:SCR_002286) | software resource | A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24681909 | Artistic License, v2 | OMICS_05601 | SCR_002286 | flowFit - Estimate proliferation in cell-tracking dye studies | 2026-09-12 12:55:39 | 4 | |||||||
|
spliceR Resource Report Resource Website 10+ mentions |
spliceR (RRID:SCR_002280) | software resource | An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. | standalone software, unix/linux, mac os x, windows, c, r, differential expression, high throughput sequencing, rna-seq, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24655717 | GNU General Public License, v2 or greater | OMICS_03514 | SCR_002280 | spliceR - Classification of alternative splicing and prediction of coding potential from RNA-seq data | 2026-09-12 12:55:39 | 25 | |||||||
|
CTCFBSDB Resource Report Resource Website 50+ mentions |
CTCFBSDB (RRID:SCR_002279) | CTCFBSDB, CTCFBSDB 2.0 | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource |
A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search. |
cctc-binding factor, ctcf, ctcf binding site, insulator, genomic insulator, genome, binding site, FASEB list |
is listed by: OMICtools has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:23193294 PMID:17981843 |
nif-0000-02703, OMICS_00530 | http://insulatordb.utmem.edu/ | SCR_002279 | CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators, CTCFBSDB 2.0: A database for CTCF binding sites and genome organization | 2026-09-12 12:55:39 | 69 | ||||||
|
FR-HIT Resource Report Resource Website 10+ mentions |
FR-HIT (RRID:SCR_002181) | FR-HIT | software resource | An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit. | metagenomics, bioinformatics, sequence analysis, next-generation sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Freely available | OMICS_01850 | SCR_002181 | FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance, Metagenome Fragment Recruitment at High Identity with Tolerance, Fragment Recruitment at High Identity with Tolerance | 2026-09-12 12:55:37 | 11 | |||||||
|
flowPlots Resource Report Resource Website |
flowPlots (RRID:SCR_002177) | software resource | Software for analysis plots and data class for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, data representation, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05608 | SCR_002177 | flowPlots: analysis plots and data class for gated flow cytometry data | 2026-09-12 12:55:37 | 0 | ||||||||
|
metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | metaRNASeq: Meta-analysis of RNA-seq data | 2026-09-12 12:55:37 | 35 | |||||||
|
DEMI Resource Report Resource Website 1+ mentions |
DEMI (RRID:SCR_002291) | software resource | R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes. | standalone software, affymetrix, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24586062 | Free, Available for download, Freely available, Acknowledgement requested | OMICS_03438 | http://cran.r-project.org/web/packages/demi/ | SCR_002291 | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-09-12 12:55:39 | 6 | ||||||
|
flowCore Resource Report Resource Website 100+ mentions |
flowCore (RRID:SCR_002205) | software resource | A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is used by: flowBeads is listed by: OMICtools has parent organization: Bioconductor |
PMID:19358741 | Artistic License, v2 | OMICS_05596 | SCR_002205 | flowCore: Basic structures for flow cytometry data | 2026-09-12 12:55:38 | 376 | |||||||
|
pFind Studio: pLink Resource Report Resource Website 10+ mentions |
pFind Studio: pLink (RRID:SCR_000084) | pLink | software resource | Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mass spectrometry, proteomics, pFind Studio, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:22772728 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02404, biotools:pLink-2 | https://github.com/pFindStudio/pLink3/releases | http://pfind.ict.ac.cn/software/pLink/index.html | SCR_000084 | , pLink, pLink (pFind Studio), pLink2 | 2026-09-12 12:55:03 | 15 | ||||
|
Spotfinder Resource Report Resource Website 1+ mentions |
Spotfinder (RRID:SCR_000085) | Spotfinder | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression. | c++ |
is listed by: OMICtools has parent organization: Dana-Farber Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00848 | SCR_000085 | TIGR Spotfinder | 2026-09-12 12:55:03 | 8 | |||||||
|
Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | Parallel META, Parallel Meta | 2026-09-12 12:55:03 | 4 | |||||||
|
BioLemmatizer Resource Report Resource Website 1+ mentions |
BioLemmatizer (RRID:SCR_000117) | software resource | A domain-specific lemmatization software tool for the morphological analysis of biomedical literature. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22464129 | Free, Available for download, Freely available | OMICS_04827 | https://sourceforge.net/projects/biolemmatizer/ | SCR_000117 | 2026-09-12 12:55:03 | 2 | |||||||
|
Orphelia Resource Report Resource Website 1+ mentions |
Orphelia (RRID:SCR_000119) | simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment. | metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment | is listed by: OMICtools | PMID:19429689 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01492 | SCR_000119 | 2026-09-12 12:55:03 | 2 | ||||||||
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ReQON Resource Report Resource Website |
ReQON (RRID:SCR_000075) | ReQON | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. | preprocessing, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22946927 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02033 | SCR_000075 | Recalibrating Quality Of Nucleotides | 2026-09-12 12:55:02 | 0 | ||||||
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QuadGT Resource Report Resource Website 1+ mentions |
QuadGT (RRID:SCR_000073) | QuadGT | software resource | Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples. | single-nucleotide variant, sequenced genome, genotype, genome |
is listed by: OMICtools has parent organization: University of Montreal; Quebec; Canada |
Normal, Tumor, Cancer | Canada National Sciences and Engineering Research Council ; Canadian Institutes for Health Research ; Terry Fox Research Institute |
PMID:23734724 | Free, Available for download, Freely available | OMICS_02108 | SCR_000073 | 2026-09-12 12:55:02 | 1 |
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