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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Sanjeevini Resource Report Resource Website 1+ mentions |
Sanjeevini (RRID:SCR_000191) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery. | drug design, molecule discovery, ligand, protein, DNA, metalloproteinase, docking, protein-ligand complex, bioinformatics | is listed by: OMICtools | PMID:23282245 | Public, Open Source | OMICS_01605 | SCR_000191 | SciCrunch Registry | 2026-10-17 01:24:34 | 1 | ||||||||
|
UnSplicer Resource Report Resource Website 1+ mentions |
UnSplicer (RRID:SCR_000226) | software resource | An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight. | RNA, sequencing, alignment, short reads, genome, genemark-es, gene prediction |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:24259430 | Free, Available for download, Freely available | OMICS_01806 | SCR_000226 | SciCrunch Registry | 2026-10-17 01:24:40 | 1 | ||||||||
|
RNAmotifs Resource Report Resource Website 1+ mentions |
RNAmotifs (RRID:SCR_000263) | RNAmotifs | software resource | Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. | rna, motif |
is listed by: OMICtools has parent organization: Bitbucket |
OMICS_02287 | https://bitbucket.org/rogrro/rna_motifs | SCR_000263 | SciCrunch Registry | rna_motifs, rna motifs | 2026-10-17 01:24:35 | 1 | |||||||
|
Quant Resource Report Resource Website |
Quant (RRID:SCR_000267) | software resource | A software tool for the proteomics community that may help improving analysis of proteomic experimental data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17584939 | Free, Available for download, Freely available | OMICS_02504, biotools:quant | https://bio.tools/quant | SCR_000267 | SciCrunch Registry | 2026-10-17 01:24:35 | 0 | |||||||
|
miRanalyzer Resource Report Resource Website 1+ mentions |
miRanalyzer (RRID:SCR_000163) | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed. | mirna, microrna, next gen sequencing, analysis, next generation, next gen, detection tool, analysis tool | is listed by: OMICtools | PMID:21515631 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00361 | SCR_000163 | SciCrunch Registry | 2026-10-17 01:24:34 | 8 | ||||||||
|
Lasergene's SeqMan Pro Resource Report Resource Website 1+ mentions |
Lasergene's SeqMan Pro (RRID:SCR_000283) | data analysis software, data processing software, data visualization software, software application, software resource | Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen. | dna, sequence, analysis, sanger, snp discovery, data visualization |
is listed by: OMICtools works with: GenVision |
Restricted | OMICS_01810 | SCR_000283 | SciCrunch Registry | Lasergenes SeqMan Pro, SeqMan Pro, SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation, DANSEUR Lasergenes SeqMan Pro | 2026-10-17 01:24:37 | 5 | ||||||||
|
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 | SciCrunch Registry | 2026-10-17 01:24:40 | 0 | |||||||
|
Grinder Resource Report Resource Website 1+ mentions |
Grinder (RRID:SCR_000168) | Grinder | software resource | An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities. | simulation, amplicon, shotgun, genomic sequencing, clinical, metagenomic, transcriptomic and metatranscriptomic |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22434876 DOI:10.1093/nar/gks251 |
Free, Available for download, Freely available | OMICS_01508 | https://sources.debian.org/src/grinder/ | SCR_000168 | SciCrunch Registry | 2026-10-17 01:24:37 | 3 | ||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | SciCrunch Registry | cn.farms - factor analysis for copy number estimation | 2026-10-17 01:24:37 | 0 | |||||
|
OMSSAPercolator Resource Report Resource Website |
OMSSAPercolator (RRID:SCR_000287) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24504981 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02524 | SCR_000287 | SciCrunch Registry | 2026-10-17 01:24:36 | 0 | ||||||||
|
CNTools Resource Report Resource Website 1+ mentions |
CNTools (RRID:SCR_000281) | CNTools | software resource | Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data. | copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02061 | SCR_000281 | SciCrunch Registry | CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses | 2026-10-17 01:24:36 | 1 | |||||||
|
GProX Resource Report Resource Website 1+ mentions |
GProX (RRID:SCR_000273) | software resource | A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21602510 | Free, Available for download, Freely available | OMICS_02506 | SCR_000273 | SciCrunch Registry | Graphical Proteomics Data Explorer | 2026-10-17 01:24:40 | 1 | |||||||
|
PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | SciCrunch Registry | 2026-10-17 01:24:36 | 4 | |||||||
|
GISTIC Resource Report Resource Website 50+ mentions |
GISTIC (RRID:SCR_000151) | GISTIC | software resource | Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category. | somatic copy-number alteration, gene |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Cancer | PMID:21527027 | Free, Available for download, Freely available | OMICS_02296 | SCR_000151 | SciCrunch Registry | GISTIC2.0, GISTIC 2.0, GISTIC 2 | 2026-10-17 01:24:37 | 58 | |||||
|
F2DockClient Resource Report Resource Website 1+ mentions |
F2DockClient (RRID:SCR_000185) | F2DockClient | software resource | A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results. | user interface, protein-protein docking, computing cluster, analysis, | is listed by: OMICtools | National Science Foundation ; National Institutes of Health |
PMID:23483883 | Free, Available for download, Freely available | OMICS_01599 | SCR_000185 | SciCrunch Registry | 2026-10-17 01:24:38 | 1 | ||||||
|
FlexX Resource Report Resource Website 1+ mentions |
FlexX (RRID:SCR_000186) | FlexX | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds. | protein binding, analysis, ligand, prediction, compounds, screening, protein-ligand docking, | is listed by: OMICtools | PMID:15382244 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01600 | SCR_000186 | SciCrunch Registry | 2026-10-17 01:24:34 | 5 | |||||||
|
RNAcontext Resource Report Resource Website 1+ mentions |
RNAcontext (RRID:SCR_000179) | RNAcontext | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website. | rna-binding protein, motif, rna sequence, rna structure, rna, binding preference, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
PMID:20617199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02253, biotools:rnacontext | https://bio.tools/rnacontext | SCR_000179 | SciCrunch Registry | 2026-10-17 01:24:34 | 2 | ||||||
|
flowMap Resource Report Resource Website 1+ mentions |
flowMap (RRID:SCR_002269) | software resource | Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process. | software package, mac os x, unix/linux, windows, r, flow cytometry, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_05600 | SCR_002269 | SciCrunch Registry | flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples | 2026-10-17 01:25:38 | 5 | ||||||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | SciCrunch Registry | 2026-10-17 01:25:34 | 11 | |||||||
|
Matchprot Resource Report Resource Website |
Matchprot (RRID:SCR_002163) | software resource | A pairwise protein structure alignment software. | standalone software, c |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17338826 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03666 | SCR_002163 | SciCrunch Registry | 2026-10-17 01:25:07 | 0 |
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