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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | SciCrunch Registry | 2026-11-07 11:57:32 | 0 | ||||||||
|
Bionotate Resource Report Resource Website 1+ mentions |
Bionotate (RRID:SCR_012098) | analysis service resource, data analysis service, production service resource, service resource, software resource | An open source annotation tool for the distributed creation of a large corpus. | web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19232400 | GNU General Public License | OMICS_05229 | SCR_012098 | SciCrunch Registry | 2026-11-07 11:57:39 | 1 | ||||||||
|
Pegasus-fus Resource Report Resource Website 10+ mentions |
Pegasus-fus (RRID:SCR_012118) | software resource | Software that annotates biologically functional gene fusion candidates. | standalone software, unix/linux, java, perl, python |
is used by: Cumulus is listed by: OMICtools has parent organization: SourceForge |
PMID:25183062 | OMICS_05584 | SCR_012118 | SciCrunch Registry | 2026-11-07 11:57:33 | 14 | |||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | SciCrunch Registry | Network Analysis and Inference Library | 2026-11-07 11:57:26 | 8 | ||||||
|
iMSAT Resource Report Resource Website 1+ mentions |
iMSAT (RRID:SCR_012135) | software resource | A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs. | standalone software, illumina, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25281214 | OMICS_05873 | SCR_012135 | SciCrunch Registry | 2026-11-07 11:57:33 | 2 | |||||||||
|
NESmapper Resource Report Resource Website 1+ mentions |
NESmapper (RRID:SCR_012138) | software resource | A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25233087 | GNU General Public License | OMICS_05911 | SCR_012138 | SciCrunch Registry | 2026-11-07 11:57:26 | 6 | ||||||||
|
DHAC Resource Report Resource Website 1+ mentions |
DHAC (RRID:SCR_012139) | software resource | Software for clustering time-evolving networks. | standalone software, c++, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22689777 | GNU General Public License | OMICS_05923 | SCR_012139 | SciCrunch Registry | Dynamical Hierarchical Agglomerative Clustering | 2026-11-07 11:57:33 | 2 | |||||||
|
xMSanalyzer Resource Report Resource Website 50+ mentions |
xMSanalyzer (RRID:SCR_012144) | software resource | A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat. | software package, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23323971 | GNU General Public License | OMICS_06039 | SCR_012144 | SciCrunch Registry | 2026-11-07 11:57:33 | 90 | ||||||||
|
EXCAVATOR-tool Resource Report Resource Website 1+ mentions |
EXCAVATOR-tool (RRID:SCR_012766) | EXCAVATOR-tool | software resource | A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00332 | SCR_012766 | SciCrunch Registry | EXCAVATOR-tool: Tool for detecting CNVs from whole-exome sequencing data | 2026-11-07 11:57:31 | 7 | |||||||||
|
miRDeep* Resource Report Resource Website 10+ mentions |
miRDeep* (RRID:SCR_012960) | miRDeep* | software resource | An integrated application software tool for miRNA identification from RNA sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221645 | GNU General Public License, v3, Acknowledgement requested | OMICS_00374 | SCR_012960 | SciCrunch Registry | 2026-11-07 11:57:33 | 23 | ||||||||
|
Trowel Resource Report Resource Website 1+ mentions |
Trowel (RRID:SCR_012890) | Trowel | software resource | An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. | c++, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Apache License | OMICS_01111, biotools:trowel | https://bio.tools/trowel/ | SCR_012890 | SciCrunch Registry | Trowel - Error Correction Module for Illumina Sequencing Reads, Trowel - Sequencing Error Corrector | 2026-11-07 11:57:32 | 5 | ||||||
|
Onco-STS Resource Report Resource Website |
Onco-STS (RRID:SCR_012990) | Onco-STS | software resource | Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01008 | SCR_012990 | SciCrunch Registry | Onco-STS - A web-based Laboratory Information Management System | 2026-11-07 11:57:57 | 0 | ||||||||
|
NxGview Resource Report Resource Website |
NxGview (RRID:SCR_012994) | NxGview | software resource | A virtual software pipeline that contains several PERL modules for processing next generation sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01065 | SCR_012994 | SciCrunch Registry | 2026-11-07 11:57:57 | 0 | ||||||||||
|
Bamformatics Resource Report Resource Website 1+ mentions |
Bamformatics (RRID:SCR_013041) | Bamformatics | software resource | Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00283 | SCR_013041 | SciCrunch Registry | Bamformatics - Toolkit and GUI for sequencing data analysis | 2026-11-07 11:57:43 | 1 | ||||||||
|
BSmapper Resource Report Resource Website |
BSmapper (RRID:SCR_012998) | BSmapper | software resource | Sequence mapper for bisulfite sequencing reads for DNA methylation studies. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00580 | SCR_012998 | SciCrunch Registry | 2026-11-07 11:57:57 | 0 | |||||||||
|
MendelScan Resource Report Resource Website 1+ mentions |
MendelScan (RRID:SCR_013053) | MendelScan | software resource | A software tool for prioritizing candidate variants in family-based studies of inherited disease. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00065 | SCR_013053 | SciCrunch Registry | MendelScan - Variant scoring and linkage mapping for family exome sequencing | 2026-11-07 11:57:42 | 4 | |||||||
|
ProbeSelect Resource Report Resource Website 1+ mentions |
ProbeSelect (RRID:SCR_012965) | ProbeSelect | software resource | Software for selecting probes in heterogenous transcriptional sets. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00836 | SCR_012965 | SciCrunch Registry | ProbeSelect - Selecting probes in heterogenous transcriptional sets | 2026-11-07 11:57:41 | 5 | |||||||||
|
SeqGenome Browser Resource Report Resource Website |
SeqGenome Browser (RRID:SCR_012970) | SeqGenome Browser | software resource | Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00924 | SCR_012970 | SciCrunch Registry | 2026-11-07 11:57:33 | 0 | ||||||||
|
miRDeep-P Resource Report Resource Website 1+ mentions |
miRDeep-P (RRID:SCR_013026) | miRDP | software resource | A computational tool for analyzing the microRNA (miRNA) transcriptome in plants. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21775303 | GNU General Public License, v3 | OMICS_00375 | SCR_013026 | SciCrunch Registry | 2026-11-07 11:57:42 | 6 | ||||||||
|
KungFq Resource Report Resource Website |
KungFq (RRID:SCR_012979) | KungFq | software resource | Tool that compresses and decompresses fastq files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221092 | OMICS_00962 | SCR_012979 | SciCrunch Registry | 2026-11-07 11:57:34 | 0 |
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