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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TileMap Resource Report Resource Website 1+ mentions |
TileMap (RRID:SCR_001589) | algorithm resource, data analysis software, data processing software, software application, software resource, source code | Software tool for microarray tile mapping. It utilizes ChIP-chip peak calling to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest. | microarray, rna, dna, sequencing, chip, tiling, chip-chip peak calling, transcription, binding |
is listed by: OMICtools works with: CisGenome |
PMID:16046496 | Free, Available for download, Freely available | OMICS_00812 | SCR_001589 | tilemapv2, TileMap Version 2 | 2026-09-19 12:49:43 | 8 | |||||||
|
asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | data analysis software, data processing software, software application, software resource, source code | Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq | r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bioconductor has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21838806 | Free, Available for download, Freely available | OMICS_01948, nlx_153893, biotools:asseq | https://bio.tools/asseq | SCR_001625 | 2026-09-19 12:49:44 | 6 | ||||||
|
GenGIS Resource Report Resource Website 10+ mentions |
GenGIS (RRID:SCR_001465) | software resource | A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. | standalone software | is listed by: OMICtools | Genome Atlantic ; Genome Canada ; Biomonitoring 2.0 Project ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation ; Natural Sciences and Engineering Research Council of Canada ; Dalhousie Faculty of Computer Science |
PMID:23922841 | Free, Available for download, Freely available | OMICS_04013 | http://kiwi.cs.dal.ca/GenGIS/ | SCR_001465 | 2026-09-19 12:49:41 | 38 | ||||||
|
ACME Resource Report Resource Website 50+ mentions |
ACME (RRID:SCR_001464) | ACME | software resource | A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. | microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:16939795 | Free, Available for download, Freely available | OMICS_01976 | SCR_001464 | Algorithms for Calculating Microarray Enrichment | 2026-09-19 12:49:41 | 62 | ||||||
|
PyLOH Resource Report Resource Website 1+ mentions |
PyLOH (RRID:SCR_001511) | software resource | Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24695406 | Free, Available for download, Freely available | OMICS_03559, biotools:pyloh | https://bio.tools/pyloh | SCR_001511 | 2026-09-19 12:49:42 | 6 | |||||||
|
CoGAPS Resource Report Resource Website 10+ mentions |
CoGAPS (RRID:SCR_001479) | CoGAPS | software resource | Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. | gene expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20810601 | Free, Available for download, Freely available | OMICS_01973 | SCR_001479 | Coordinated Gene Activity in Pattern Sets | 2026-09-19 12:49:41 | 38 | ||||||
|
Nebula Resource Report Resource Website 10+ mentions |
Nebula (RRID:SCR_001516) | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web portal that allows users to analyze ChIP-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web portal, chip-seq data, online analysis tool |
uses: Galaxy is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
PMID:22829625 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00424 | SCR_001516 | Nebula - A web-server for advanced ChIP-seq data analysis | 2026-09-19 12:49:43 | 24 | |||||||
|
ChIPseeqer Resource Report Resource Website 10+ mentions |
ChIPseeqer (RRID:SCR_001545) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that provides a comprehensive framework for the analysis of ChIP-seq data. | sequence analysis, framework, ChIP, chip-seq, chip-seq data, sequencing, data, algorithm |
is listed by: OMICtools has parent organization: Weill Cornell Medical College; New York; USA |
DOI:10.1186/1471-2105-12-277 | Free, Available for download, Freely available | OMICS_00422 | SCR_001545 | 2026-09-19 12:49:42 | 18 | ||||||||
|
flowFP Resource Report Resource Website 1+ mentions |
flowFP (RRID:SCR_001537) | software resource | A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956416 | Free, Available for download, Freely available | OMICS_05599 | SCR_001537 | flowFP - Fingerprinting for Flow Cytometry | 2026-09-19 12:49:43 | 4 | |||||||
|
MCMC.qpcr Resource Report Resource Website 10+ mentions |
MCMC.qpcr (RRID:SCR_001721) | software resource | Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977043 | Free, Available for download, Freely available | OMICS_03934 | SCR_001721 | MCMC.qpcr: Bayesian analysis of qRT-PCR data | 2026-09-19 12:49:45 | 24 | |||||||
|
rSeqDiff Resource Report Resource Website |
rSeqDiff (RRID:SCR_001683) | rSeqDiff | software resource | An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing. | rna-seq, gene expression, differential expression, differential splicing, gene |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24260225 | Free, Available for download, Freely available | OMICS_01968 | SCR_001683 | rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test | 2026-09-19 12:49:45 | 0 | ||||||
|
QuasiSeq Resource Report Resource Website 10+ mentions |
QuasiSeq (RRID:SCR_001715) | QuasiSeq | software resource | Software package to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data. | differential expression, gene, rna-seq, next generation sequencing, gene expression, mrna | is listed by: OMICtools | PMID:23104842 | Free, Available for download, Freely available | OMICS_01963 | http://cran.r-project.org/web/packages/QuasiSeq/index.html | SCR_001715 | 2026-09-19 12:49:45 | 20 | ||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | data or information resource, database, software resource | Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-09-19 12:49:46 | 0 | ||||||
|
TANGO Resource Report Resource Website 100+ mentions |
TANGO (RRID:SCR_001770) | TANGO | software resource | A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions. | polypeptide chain, polypeptide, peptide, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:15361882 | Free, Freely available | biotools:tango, OMICS_03859 | https://bio.tools/tango | SCR_001770 | 2026-09-19 12:49:46 | 136 | ||||||
|
MSClust Resource Report Resource Website 10+ mentions |
MSClust (RRID:SCR_001773) | MSClust | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An M software package for Clustering 16S rRNA sequences into operational taxonomic units (OTUs). The download link contain the package and some benchmark data sets. | 16s rrna, operational taxonomic unit, 16s rrna read, clustering algorithm, next-generation sequencing, seeds-selection |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:23899776 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_01954 | http://bioinformatics.med.yale.edu/group/ | SCR_001773 | 2026-09-19 12:49:48 | 32 | ||||||
|
BLASTX Resource Report Resource Website 10000+ mentions |
BLASTX (RRID:SCR_001653) | BLASTX | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. | protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
PMID:28902395 PMID:8485583 |
Free, Freely Available | nlx_153933, OMICS_00992 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001653 | Translated BLAST, Translated BLAST: blastx | 2026-09-19 12:49:44 | 10411 | |||||
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Cuffdiff Resource Report Resource Website 1000+ mentions |
Cuffdiff (RRID:SCR_001647) | Cuffdiff | software resource | Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. | differential expression, rna-seq, transcript, splicing, promoter, coding sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Cufflinks has parent organization: University of Maryland; Maryland; USA |
PMID:23222703 | Free, Available for download, Freely available | biotools:cuffdiff, OMICS_01969 | https://bio.tools/cuffdiff | SCR_001647 | Cuffdiff 2 | 2026-09-19 12:49:44 | 3925 | |||||
|
PennSeq Resource Report Resource Website 1+ mentions |
PennSeq (RRID:SCR_001763) | PennSeq | software resource | Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. | isoform, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24362841 | Free, Available for download, Freely available | biotools:pennseq, OMICS_01946 | https://bio.tools/pennseq | SCR_001763 | 2026-09-19 12:49:46 | 4 | ||||||
|
MACH 1.0 Resource Report Resource Website 50+ mentions |
MACH 1.0 (RRID:SCR_001759) | data analysis software, data processing software, software application, software resource | A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. | gene, genetic, genomic, haplotype, genotype, genomic analysis, imaging genomics, imputation, snp, gene, haplotyping, sequence |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mach2dat has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 |
Free | nlx_154202, OMICS_00064 | SCR_001759 | MArkov Chain Haplotyper MINIMAC, MArkov Chain Haplotyping | 2026-09-19 12:49:47 | 58 | |||||||
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GLiMMPS Resource Report Resource Website 1+ mentions |
GLiMMPS (RRID:SCR_001787) | GLiMMPS | software resource | Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. | alternative splicing, rna-seq, genetic variation, splicing quantitative trait loci |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:23876401 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01947 | SCR_001787 | 2026-09-19 12:49:47 | 2 |
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