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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Batman-Seq Resource Report Resource Website |
Batman-Seq (RRID:SCR_000048) | Batman-Seq | software resource | A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment. | c++ | is hosted by: SourceForge | Free, Available for download, Freely available | OMICS_00651 | SCR_000048 | Basic Alignment Tool for MAny Nucleotides | 2026-07-25 12:04:34 | 0 | |||||||
|
MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | Mass Spectrometry Analysis Software | 2026-07-25 12:04:39 | 1 | ||||||||
|
BLASTPLOT Resource Report Resource Website |
BLASTPLOT (RRID:SCR_000162) | BLASTPLOT | software resource | A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set. | perl, blast, short sequence, primer, png, png graph |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24685334 | Free, Available for download, Freely available | OMICS_01433 | SCR_000162 | 2026-07-25 12:04:37 | 0 | |||||||
|
GemSIM Resource Report Resource Website |
GemSIM (RRID:SCR_000167) | GemSIM | software resource | A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface. | bioinformatics, simulation, sequencing, dna, rna, empirical models, Python, command-line, user interface, metagenomic, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: Wessim |
PMID:22336055 DOI:10.1186/1471-2164-13-74 |
Free, Available for download, Freely available | OMICS_01507, biotools:GemSIM | https://bio.tools/GemSIM | SCR_000167 | 2026-07-25 12:04:37 | 0 | ||||||
|
ProteinProphet Resource Report Resource Website 10+ mentions |
ProteinProphet (RRID:SCR_000286) | software resource | Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra 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:14632076 | OMICS_02521, biotools:proteinprophet | https://bio.tools/proteinprophet | SCR_000286 | 2026-07-25 12:04:42 | 10 | ||||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2026-07-25 12:04:43 | 2 | |||||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | 2026-07-25 12:04:43 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | 2026-07-25 12:04:43 | 2 | ||||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | 2026-07-25 12:04:43 | 0 | |||||||||
|
fqzcomp Resource Report Resource Website 1+ mentions |
fqzcomp (RRID:SCR_000299) | fqzcomp | software resource | A basic fastq compressor, designed primarily for high performance. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00957 | SCR_000299 | 2026-07-25 12:04:41 | 1 | |||||||
|
miRprimer Resource Report Resource Website 1+ mentions |
miRprimer (RRID:SCR_000480) | miRprimer | software resource | Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70). | ruby, primer, microrna, rt-qpcr, ms windows, pcr amplification |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24472427 | Free, Available for download, Freely available | OMICS_02311 | SCR_000480 | miRprimer - Automatic design of primers for miR-specific RT-qPCR | 2026-07-25 12:04:45 | 3 | ||||||
|
pyQPCR Resource Report Resource Website |
pyQPCR (RRID:SCR_000471) | pyQPCR | software resource | A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu | quantitative pcr, python, qt |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02326 | SCR_000471 | 2026-07-25 12:04:45 | 0 | ||||||||
|
drFAST Resource Report Resource Website 1+ mentions |
drFAST (RRID:SCR_000586) | drFAST | software resource | A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner. | di-base, solid color space, genome assemblies, memory-efficient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:21586516 | Free, Available for download, Freely available | biotools:drfast, OMICS_00661 | https://bio.tools/drfast | SCR_000586 | di-base read Fast Alignment Search Tool, drFAST: di-base read Fast Alignment Search Tool | 2026-07-25 12:04:47 | 1 | |||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | biotools:maq, OMICS_00668 | https://bio.tools/maq, https://sources.debian.org/src/maq/ | SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-07-25 12:06:05 | 69 | |||||
|
MACE Resource Report Resource Website 1000+ mentions |
MACE (RRID:SCR_005520) | MACE | software resource | A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00520 | SCR_005520 | MACE: Model based Analysis of ChIP-exo | 2026-07-25 12:06:06 | 1172 | |||||||||
|
TreQ Resource Report Resource Website |
TreQ (RRID:SCR_005505) | TreQ | software resource | A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Rutgers University; New Jersey; USA |
PMID:22962448 | GNU General Public License | OMICS_00695, biotools:treq | https://bio.tools/treq | SCR_005505 | TreQ: Indel-tolerant Read Mapper | 2026-07-25 12:06:07 | 0 | |||||
|
netClass Resource Report Resource Website |
netClass (RRID:SCR_005672) | netClass | software resource | An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). | protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24443376 | Free, Public | OMICS_02241 | SCR_005672 | 2026-07-25 12:06:08 | 0 | |||||||
|
TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-07-25 12:06:09 | 10 | ||||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-07-25 12:06:06 | 79 | ||||||
|
MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-07-25 12:06:11 | 456 |
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