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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
enviPat Resource Report Resource Website 10+ mentions |
enviPat (RRID:SCR_003034) | software resource | Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Freely available | OMICS_02408 | SCR_003034 | enviPat: Isotope pattern profile and centroid calculation for mass spectrometry | 2026-09-05 06:24:57 | 33 | ||||||||
|
MoSDi Resource Report Resource Website 1+ mentions |
MoSDi (RRID:SCR_003037) | data analysis software, data processing software, software application, software resource, software toolkit | Sequence analysis toolkit that contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of motifs with provably optimal p-value, 3) analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text, 4) statistics of fragment masses resulting from proteolytic cleavage of proteins, 5) computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent) and 6) analysing sensitivity of spaced alignment seeds. | standalone software, unix/linux, motif |
is listed by: OMICtools has parent organization: Google Code |
PMID:19478010 | Free, Freely available | OMICS_06271 | https://bio.tools/mosdi | SCR_003037 | Motif Statistics and Discovery, Motif Statistics and Discovery - Sequence analysis toolkit for bioinformatics | 2026-09-05 06:24:57 | 2 | ||||||
|
SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SMRT-View | 2026-09-05 06:24:56 | 9 | |||||||
|
QDNAseq Resource Report Resource Website 100+ mentions |
QDNAseq (RRID:SCR_003174) | software resource | Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively. | software package, unix/linux, mac os x, windows, r, copy number variation, dna-seq, genetics, genome annotation, preprocessing, quality control, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25236618 | Free, Available for download, Freely available | OMICS_05902, biotools:qdnaseq | https://github.com/ccagc/QDNAseq, https://bio.tools/qdnaseq | SCR_003174 | QDNAseq - Quantitative DNA sequencing for chromosomal aberrations | 2026-09-05 06:24:59 | 168 | ||||||
|
ABS filter Resource Report Resource Website |
ABS filter (RRID:SCR_005328) | ABS filter | software resource | R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. | unix/linux |
is listed by: OMICtools has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland |
PMID:24255646 | GNU General Public License, v3 | OMICS_00427 | SCR_005328 | R package - ABS filter, absfilter | 2026-09-05 06:25:33 | 0 | ||||||
|
APSampler Resource Report Resource Website |
APSampler (RRID:SCR_000042) | software resource | A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data. | mac os x, unix/linux, windows, c, c++, perl | has parent organization: Google Code | PMID:16118183 | Free, Available for download, Freely available | OMICS_04023 | http://code.google.com/p/apsampler/ | SCR_000042 | 2026-09-05 06:24:09 | 0 | |||||||
|
MetaDE Resource Report Resource Website 1+ mentions |
MetaDE (RRID:SCR_000199) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:22863766 | Free, Available for download, Freely available | OMICS_04033 | http://cran.r-project.org/web/packages/MetaDE/ | SCR_000199 | MetaDE: Microarray meta-analysis for differentially expressed gene detection | 2026-09-05 06:24:14 | 1 | ||||||
|
Flicker Resource Report Resource Website |
Flicker (RRID:SCR_000288) | software resource | An open-source stand-alone computer program for visually comparing 2D gel images. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:10027264 | Free, Available for download, Freely available | OMICS_02538, biotools:nci_flicker | https://bio.tools/nci_flicker | SCR_000288 | 2026-09-05 06:24:16 | 0 | |||||||
|
cuteNMR Resource Report Resource Website |
cuteNMR (RRID:SCR_000347) | software resource | A multi-platform NMR processing application. | standalone software, mac os x, unix/linux, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_03391 | SCR_000347 | 2026-09-05 06:24:17 | 0 | |||||||||
|
JMolDraw Resource Report Resource Website |
JMolDraw (RRID:SCR_000349) | software resource | 2-D chemical structure drawing software program. | applet, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_05000 | SCR_000349 | 2026-09-05 06:24:19 | 0 | |||||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-09-05 06:24:19 | 21 | |||||||
|
flowStats Resource Report Resource Website 1+ mentions |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-09-05 06:24:19 | 1 | ||||||||
|
FACIL Resource Report Resource Website 1+ mentions |
FACIL (RRID:SCR_004375) | FACIL | analysis service resource, data analysis service, production service resource, service resource, software resource | Genetic code prediction tool that infers the genetic code directly from any set of nucleic acid sequences and assigns a Random Forest-based reliability score to its predictions. | unix/linux | is listed by: OMICtools | PMID:21653513 | Commercial license, Free | OMICS_00299 | SCR_004375 | FACIL genetic code prediction tool, Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo | 2026-09-05 06:29:57 | 9 | ||||||
|
Phosphor Antibody Array Data Analysis Resource Report Resource Website |
Phosphor Antibody Array Data Analysis (RRID:SCR_000633) | PANDA | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies. | unix/linux, windows |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA |
PMID:18794113 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04025 | SCR_000633 | PANDA: Phosphor Antibody Array Data Analysis | 2026-09-05 06:31:11 | 0 | ||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-09-05 06:32:20 | 0 | ||||||
|
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 | heurAA - NGS multiplexed amplicon aligner | 2026-09-05 06:27:33 | 0 | ||||||
|
orthAgogue Resource Report Resource Website 10+ mentions |
orthAgogue (RRID:SCR_011979) | orthAgogue | software resource | A software tool for high speed estimation of homology relations within and between species in massive data sets. | unix/linux |
is listed by: OMICtools has parent organization: Google Code |
PMID:24115168 | GNU General Public License, v3 | OMICS_01691 | SCR_011979 | orthAgogue: a tool for high speed estimation of homology relations within and between species in massive data sets. | 2026-09-05 06:27:17 | 32 | ||||||
|
Eoulsan Resource Report Resource Website 10+ mentions |
Eoulsan (RRID:SCR_011901) | Eoulsan | software resource | A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. | matlab, unix/linux, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22492314 | OMICS_01402, biotools:Eoulsan | https://www.outils.genomique.biologie.ens.fr/eoulsan/, https://bio.tools/Eoulsan | SCR_011901 | 2026-09-05 06:27:15 | 22 | |||||||
|
QuteMol Resource Report Resource Website 10+ mentions |
QuteMol (RRID:SCR_012089) | software resource | Open source (GPL) software providing an interactive, high quality molecular visualization system. | standalone software, unix/linux, windows |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:17080857 DOI:10.1109/TVCG.2006.115 |
Free, Freely available | OMICS_05075 | https://sources.debian.org/src/qutemol/ | SCR_012089 | 2026-09-05 06:27:20 | 14 | |||||||
|
PRIDE Converter 2 Resource Report Resource Website 1+ mentions |
PRIDE Converter 2 (RRID:SCR_012051) | software resource | Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra. | standalone software, mac os x, unix/linux, windows, java, xml, mass spectrometry, pride, ols, proteomics, psi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Google Code |
PMID:22949509 | Apache License, v2 | biotools:pride_converter, OMICS_03344 | https://bio.tools/pride_converter | SCR_012051 | PRIDE, PRoteomics IDEntification (PRIDE) Converter 2 | 2026-09-05 06:27:19 | 1 |
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