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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-11-07 11:53:56 | 0 | |||||||
|
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 | 2026-11-07 11:53:56 | 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 | 2026-11-07 11:53:53 | 3 | ||||||
|
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 | 2026-11-07 11:53:57 | 0 | ||||||||
|
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 | 2026-11-07 11:53:55 | 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 | 2026-11-07 11:53:58 | 4 | |||||||
|
CGAP-Align Resource Report Resource Website |
CGAP-Align (RRID:SCR_000350) | software resource | A time efficient read alignment tool built on the top of BWA. | standalone software, illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23593381 | Free, Available for download, Freely available | OMICS_05480 | SCR_000350 | SciCrunch Registry | 2026-11-07 11:53:58 | 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 | SciCrunch Registry | 2026-11-07 11:53:57 | 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 | SciCrunch Registry | 2026-11-07 11:54:02 | 0 | |||||||||
|
AS-Peak Resource Report Resource Website 1+ mentions |
AS-Peak (RRID:SCR_000380) | ASPeak | software resource | A software that utilizes a peak detection algorithm to identify RNA-protein binding sites. | rna, peak detection, protein, binding, site, algorithm, analysis |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23929032 | Free, Available for download, Freely available | OMICS_00566 | https://omictools.com/aspeak-tool | SCR_000380 | SciCrunch Registry | 2026-11-07 11:54:04 | 2 | ||||||
|
GENSENG Resource Report Resource Website 1+ mentions |
GENSENG (RRID:SCR_000378) | data analysis software, data processing software, software application, software resource | Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders. | next generation sequencing data, detecting copy number variations, discrete copy number changes, identify regions |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23275535 | Free, Available for download, Freely available | OMICS_00345 | SCR_000378 | SciCrunch Registry | 2026-11-07 11:53:58 | 1 | ||||||||
|
D-Tailor Resource Report Resource Website |
D-Tailor (RRID:SCR_000115) | software resource | A fully extendable software framework, for property-based design of synthetic DNA sequences. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24398007 | Free, Available for download, Freely available | OMICS_04768 | SCR_000115 | SciCrunch Registry | DNA-Tailor | 2026-11-07 11:53:53 | 0 | |||||||
|
siRNArules Resource Report Resource Website |
siRNArules (RRID:SCR_000096) | software resource | An open-source JAVA program that is surprisingly efficient at predicting active siRNAs. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:16870995 | Free, Available for download, Freely available | OMICS_04742 | SCR_000096 | SciCrunch Registry | 2026-11-07 11:53:53 | 0 | ||||||||
|
AbMining ToolBox Resource Report Resource Website |
AbMining ToolBox (RRID:SCR_000090) | software resource | Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq). | standalone software, illumina, roche, life technologies, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24423623 | Free, Available for download, Freely available | OMICS_04063 | SCR_000090 | SciCrunch Registry | 2026-11-07 11:53:52 | 0 | ||||||||
|
SP-Designer Resource Report Resource Website |
SP-Designer (RRID:SCR_000031) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. | standalone software, windows |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23634845 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03932 | SCR_000031 | SciCrunch Registry | 2026-11-07 11:53:50 | 0 | ||||||||
|
MysiRNA-designer Resource Report Resource Website |
MysiRNA-designer (RRID:SCR_000102) | software resource | Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22046244 | Free, Available for download, Freely available | OMICS_04748 | SCR_000102 | SciCrunch Registry | 2026-11-07 11:53:53 | 0 | ||||||||
|
dprimer Resource Report Resource Website |
dprimer (RRID:SCR_000050) | dprimer | software resource | A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample. | c++, command-line, pcr, primer, aligned sequence, degenerate primer | has parent organization: SourceForge | Free, Available for download, Freely available | OMICS_02342 | SCR_000050 | SciCrunch Registry | 2026-11-07 11:53:51 | 0 | ||||||||
|
iMethy Resource Report Resource Website |
iMethy (RRID:SCR_000049) | iMethy | software resource | Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing. | matlab | has parent organization: SourceForge | Free, Available for download, Freely available | OMICS_00628 | SCR_000049 | SciCrunch Registry | 2026-11-07 11:53:51 | 0 | ||||||||
|
EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | SciCrunch Registry | 2026-11-07 11:57:33 | 2 | ||||||||||
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | SciCrunch Registry | 2026-11-07 11:57:29 | 2 |
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