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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PGS Resource Report Resource Website |
PGS (RRID:SCR_000475) | software resource | Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24947752 | Free, Available for download, Freely available | biotools:pgs, OMICS_04651 | https://bio.tools/pgs | SCR_000475 | PGS: Penalized GEE with Grid Search, Penalized GEE with Grid Search | 2026-02-07 02:05:22 | 0 | ||||||
|
SpeedSeq Resource Report Resource Website 1+ mentions |
SpeedSeq (RRID:SCR_000469) | software resource | Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)). | standalone software |
is listed by: OMICtools has parent organization: University of Virginia; Virginia; USA |
Free, Available for download, Freely available | OMICS_04673 | SCR_000469 | 2026-02-07 02:05:23 | 7 | |||||||||
|
MATCHCLIP Resource Report Resource Website |
MATCHCLIP (RRID:SCR_000541) | MATCHCLIP | software resource | Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide. | breakpoint, deletion, duplication, exon sequencing, structural variation, next generation sequencing |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:23967014 | Free, Available for download, Freely available, | OMICS_02289 | SCR_000541 | matchclips2, MATCHCLIPS | 2026-02-07 02:05:21 | 0 | ||||||
|
TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-02-07 02:05:23 | 0 | |||||||
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-02-07 02:05:23 | 13 | |||||
|
Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-02-07 02:05:24 | 22 | ||||||
|
SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-02-07 02:05:23 | 6 | ||||||
|
TNO-DECO Resource Report Resource Website |
TNO-DECO (RRID:SCR_000440) | software resource | Matlab code for preprocessing gas chromatography mass spectrometry data. | matlab, mass spectrometry | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02660 | SCR_000440 | 2026-02-07 02:05:20 | 0 | |||||||||
|
SNPiR Resource Report Resource Website 1+ mentions |
SNPiR (RRID:SCR_000557) | SNPiR | software resource | Software for reliable Identification of Genomic Variants Using RNA-seq Data. | genomic variant, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01362 | SCR_000557 | SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data | 2026-02-07 02:05:24 | 1 | |||||||
|
FPSAC Resource Report Resource Website 1+ mentions |
FPSAC (RRID:SCR_000555) | FPSAC | software resource | Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs. | genome, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:24068034 | biotools:fpsac, OMICS_00041 | https://bio.tools/fpsac | SCR_000555 | Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent, Fast Phylogenetic Scaffolding of Ancient Contigs, FPSAC: fast phylogenetic scaffolding of ancient contigs | 2026-02-07 02:05:21 | 1 | ||||||
|
ACCUSA2 Resource Report Resource Website |
ACCUSA2 (RRID:SCR_000558) | ACCUSA2 | software resource | Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores. | snv | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01360 | SCR_000558 | 2026-02-07 02:05:21 | 0 | ||||||||
|
DySC Resource Report Resource Website |
DySC (RRID:SCR_000553) | DySC | software resource | Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy. | cluster, 16s rrna, read |
is listed by: OMICtools has parent organization: Google Code |
PMID:22730435 | Free, Available for download, Freely available, | OMICS_01443 | SCR_000553 | DySC: Software for Greedy Clustering of 16S rRNA Reads | 2026-02-07 02:05:23 | 0 | ||||||
|
drFAST Resource Report Resource Website 1+ mentions |
drFAST (RRID:SCR_000586) | drFAST | software resource | A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner. | di-base, solid color space, genome assemblies, memory-efficient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:21586516 | Free, Available for download, Freely available | biotools:drfast, OMICS_00661 | https://bio.tools/drfast | SCR_000586 | di-base read Fast Alignment Search Tool, drFAST: di-base read Fast Alignment Search Tool | 2026-02-07 02:05:24 | 1 | |||||
|
Genome BioInformatics Research Lab - gff2ps Resource Report Resource Website 1+ mentions |
Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format. | genome, sequence, visualization, parameters, bioinformatics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:11099262 DOI:10.1093/bioinformatics/16.8.743 |
Free, Available for download, Freely available | OMICS_17140, biotools:gff2ps, nif-0000-30611 | https://bio.tools/gff2ps https://sources.debian.org/src/gff2ps/ |
SCR_000462 | gff2ps | 2026-02-07 02:05:22 | 1 | ||||||
|
NGSmethPipe Resource Report Resource Website 1+ mentions |
NGSmethPipe (RRID:SCR_000583) | NGSmethPipe | software resource | A software tool which generates high-quality methylation maps. | computation, genomics, bioinformatics, methylation maps, visualization |
is listed by: OMICtools has parent organization: University of Granada; Granada; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00611 | SCR_000583 | NGSmethPipe - A tool to generate high-quality methylation maps | 2026-02-07 02:05:21 | 3 | |||||||
|
sybil - Efficient Constrained Based Modelling in R Resource Report Resource Website |
sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) | sybil | software resource | A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language. | unix/linux, windows, r |
is listed by: OMICtools is related to: SBML is related to: CRAN |
PMID:24224957 | Free, Available for download, Freely available | OMICS_06008 | http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html | http://cran.r-project.org/web/packages/sybil/index.html | SCR_000457 | sybil: sybil - Efficient Constrained Based Modelling in R | 2026-02-07 02:05:20 | 0 | ||||
|
msbwt Resource Report Resource Website |
msbwt (RRID:SCR_000458) | software resource | A software package for creating, merging, and querying multi-string BWTs. | standalone software, python |
is listed by: OMICtools has parent organization: Google Code |
PMID:25172922 | Free, Available for download, Freely available | OMICS_05976 | https://code.google.com/p/msbwt/ | SCR_000458 | multi-string BWT | 2026-02-07 02:05:22 | 0 | ||||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop https://bio.tools/rdisop |
SCR_000453 | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-02-07 02:05:22 | 0 | |||||||
|
stsPlots Resource Report Resource Website |
stsPlots (RRID:SCR_000449) | software resource | Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems. | software package, r | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05141 | SCR_000449 | 2026-02-07 02:05:22 | 0 | |||||||||
|
ContEst Resource Report Resource Website 1+ mentions |
ContEst (RRID:SCR_000595) | ContEst | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. | java, contamination, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:21803805 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01038, biotools:contest | https://bio.tools/contest | SCR_000595 | 2026-02-07 02:05:23 | 5 |
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