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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VegaMC Resource Report Resource Website 1+ mentions |
VegaMC (RRID:SCR_001267) | VegaMC | software resource | Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported. | copy number variation, acgh, chromosomal imbalance |
is listed by: OMICtools is related to: PennCNV has parent organization: Bioconductor |
Cancer | PMID:22815357 | Free, Available for download, Freely available | OMICS_02071 | SCR_001267 | VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer | 2026-09-05 06:24:32 | 1 | |||||
|
VanillaICE Resource Report Resource Website 1+ mentions |
VanillaICE (RRID:SCR_001268) | VanillaICE | software resource | Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. | statistics, dna copy number, snp, genetic variability, visualization, high throughput, snp chip, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:19609370 | GNU General Public License, v2 or newer | OMICS_02070 | http://www.biostat.jhsph.edu/~rscharpf/software/index.html | SCR_001268 | vanilla-ice | 2026-09-05 06:24:32 | 3 | |||||
|
Mutascope Resource Report Resource Website 1+ mentions |
Mutascope (RRID:SCR_001265) | Mutascope | data analysis software, data processing software, software application, software resource | Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. | high throughput sequencing, pcr amplicon, pcr, mutation, amplicon, sequencing, somatic variant |
is listed by: OMICtools has parent organization: SourceForge |
Tumor, Normal | PMID:23712659 | Free, Public | OMICS_02074 | SCR_001265 | Mutascope - Analysis software designed for PCR-amplicon sequencing data | 2026-09-05 06:24:32 | 4 | |||||
|
GemTools Resource Report Resource Website 10+ mentions |
GemTools (RRID:SCR_001259) | GemTools | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R. | genetic, ancestry, single nucleotide polymorphism, r |
is listed by: OMICtools has parent organization: University of Pittsburgh; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02079 | SCR_001259 | GemTools - A fast and efficient approach to estimating genetic ancestry | 2026-09-05 06:24:31 | 45 | |||||||
|
SCAN.UPC Resource Report Resource Website 10+ mentions |
SCAN.UPC (RRID:SCR_001334) | SCAN.UPC | software resource | A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A | microarray, one channel, preprocessing, rna-seq, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02006 | SCR_001334 | Single-channel array normalization (SCAN) and Universal exPression Codes (UPC), Single-channel array normalization and Universal exPression Codes | 2026-09-05 06:24:33 | 11 | |||||||
|
betr Resource Report Resource Website 10+ mentions |
betr (RRID:SCR_001332) | betr | software resource | Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data. | differentially expression, gene, microarray, time-course |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20003283 | Free, Available for download, Freely available | OMICS_01997 | http://www.bioconductor.org/packages/release/bioc/html/betr.html | SCR_001332 | Bayesian Estimation of Temporal Regulation | 2026-09-05 06:24:33 | 17 | |||||
|
PiMS Resource Report Resource Website 100+ mentions |
PiMS (RRID:SCR_011816) | PiMS | software resource | Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes. | protein | is listed by: OMICtools | BBSRC ; CCP4 ; Instruct |
PMID:21385349 | Free for academic use | OMICS_01010 | SCR_011816 | Protein Information Management System | 2026-09-05 06:27:13 | 190 | |||||
|
Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | data or information resource, database, software resource | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-09-05 06:27:12 | 6 | |||||||||
|
B-Fabric Resource Report Resource Website 1+ mentions |
B-Fabric (RRID:SCR_011827) | B-Fabric | data or information resource, data repository, database, service resource, storage service resource | An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis. | project management, mass spectrometry, protein sequencing, peptide sequencing, amino acid analysis, chromatography, electrophoresis |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:21772064 | Account required | OMICS_01002 | SCR_011827 | 2026-09-05 06:27:13 | 1 | |||||||
|
Galaxy LIMS Resource Report Resource Website |
Galaxy LIMS (RRID:SCR_011829) | Galaxy LIMS | software resource | A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. | is listed by: OMICtools | BMBF | PMID:23479349 | OMICS_01004 | SCR_011829 | 2026-09-05 06:27:13 | 0 | ||||||||
|
GPU-BLAST Resource Report Resource Website |
GPU-BLAST (RRID:SCR_011820) | GPU-BLAST | software resource | Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries. | c++, gpu/cuda |
is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA |
PMID:21088027 | Free, Public, Acknowledgement requested | OMICS_00995 | http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html | SCR_011820 | 2026-09-05 06:27:13 | 0 | ||||||
|
TBLASTX Resource Report Resource Website 1000+ mentions |
TBLASTX (RRID:SCR_011823) | TBLASTX | software resource, web application | A web-based tool used to search translated nucleotide databases using a translated nucleotide query. | nucleotide database, web based, nucleotide query |
is listed by: OMICtools has parent organization: NCBI |
Available to the research community | OMICS_01000 | SCR_011823 | Translated BLAST: tblastx | 2026-09-05 06:27:13 | 1467 | |||||||
|
IGB Resource Report Resource Website 100+ mentions |
IGB (RRID:SCR_011792) | IGB | software resource | An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more. | genome, rna-seq, chip-seq, tiling array, browser |
is listed by: OMICtools has parent organization: University of North Carolina at Charlotte; North Carolina; USA |
PMID:19654113 | Free, Acknowledgement requested | OMICS_00916 | SCR_011792 | Integrated Genome Browser | 2026-09-05 06:27:12 | 354 | ||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv, https://sources.debian.org/src/igv/ | SCR_011793 | 2026-09-05 06:27:12 | 878 | |||||||
|
NCBI Genome Workbench Resource Report Resource Website 10+ mentions |
NCBI Genome Workbench (RRID:SCR_011794) | Genome Workbench | software resource | An integrated application for viewing and analyzing sequence data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
OMICS_00920, biotools:ncbi_genome_workbench | https://bio.tools/ncbi_genome_workbench | SCR_011794 | 2026-09-05 06:27:13 | 11 | ||||||||
|
ngs.plot Resource Report Resource Website 10+ mentions |
ngs.plot (RRID:SCR_011795) | ngs.plot | software resource | A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. | bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
GNU General Public License, v3 | BioTools:ngs.plot, OMICS_00922, biotools:ngs.plot | https://bio.tools/ngs.plot, https://bio.tools/ngs.plot, https://bio.tools/ngs.plot | SCR_011795 | ngsplot, ngsplot - Quick mining and visualization of next-generation sequencing data by integrating genomic databases | 2026-09-05 06:27:12 | 45 | ||||||
|
MizBee Resource Report Resource Website 1+ mentions |
MizBee (RRID:SCR_011804) | MizBee | software resource | A multiscale synteny browser for exploring conservation relationships in comparative genomics data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
OMICS_00943, biotools:mizbee | https://bio.tools/mizbee | SCR_011804 | MizBee - A Multiscale Synteny Browser | 2026-09-05 06:27:12 | 2 | |||||||
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PipMaker and MultiPipMaker Resource Report Resource Website 50+ mentions |
PipMaker and MultiPipMaker (RRID:SCR_011806) | PipMaker and MultiPipMaker | software resource | PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results. |
is listed by: OMICtools has parent organization: Pennsylvania State University |
OMICS_00944 | SCR_011806 | 2026-09-05 06:27:12 | 78 | ||||||||||
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SynBrowse Resource Report Resource Website 1+ mentions |
SynBrowse (RRID:SCR_011807) | SynBrowse | software resource | A generic sequence comparison tool for visualizing genome alignments both within and between species. | is listed by: OMICtools | OMICS_00946 | SCR_011807 | Synteny Browser | 2026-09-05 06:27:13 | 2 | |||||||||
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ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-09-05 06:27:14 | 312 |
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