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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ORMAN Resource Report Resource Website 1+ mentions |
ORMAN (RRID:SCR_005188) | ORMAN | software resource | A software tool for resolving multi-mappings within an RNA-Seq SAM file. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24130305 | OMICS_01284, biotools:orman | https://bio.tools/orman | SCR_005188 | ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms | 2026-08-01 12:02:57 | 4 | ||||||
|
Ergatis Resource Report Resource Website 1+ mentions |
Ergatis (RRID:SCR_005377) | Ergatis | software resource | A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level. | workflow, bioinformatics, workflow management, pipeline, computation, genomics, genome, processing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:20413634 | Artistic License | OMICS_01140 | SCR_005377 | ergatis: workflow creation and monitoring interface | 2026-08-01 12:02:51 | 2 | ||||||
|
MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-08-01 12:02:53 | 0 | |||||||
|
SPLITREAD Resource Report Resource Website 1+ mentions |
SPLITREAD (RRID:SCR_005264) | SPLITREAD | software resource | Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data. | deletion, insertion, indel, genome, exome |
is listed by: OMICtools is related to: drFAST is related to: mrFAST is related to: mrsFAST is related to: VariationHunter is related to: NovelSeq is related to: mrCaNaVaR has parent organization: SourceForge |
OMICS_00323 | SCR_005264 | SPLITREAD - Split read based INDEL/SV Caller | 2026-08-01 12:02:58 | 3 | ||||||||
|
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 | 2026-08-01 12:02:59 | 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 | 2026-08-01 12:03:00 | 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 | 2026-08-01 12:02:53 | 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 | 2026-08-01 12:03:01 | 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 | 2026-08-01 12:02:55 | 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 | 2026-08-01 12:02:57 | 79 | ||||||
|
diCal-IBD Resource Report Resource Website |
diCal-IBD (RRID:SCR_012111) | software resource | Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. | standalone software, unix/linux, mac os x, windows, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25147361 | BSD License | OMICS_05459 | SCR_012111 | 2026-08-01 12:04:35 | 0 | ||||||||
|
Ionwinze Resource Report Resource Website |
Ionwinze (RRID:SCR_012115) | software resource | Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures. | standalone software, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24004415 | GNU General Public License | OMICS_05522 | SCR_012115 | 2026-08-01 12:04:34 | 0 | ||||||||
|
GenoSIGHT Resource Report Resource Website |
GenoSIGHT (RRID:SCR_012119) | software resource | An adaptive imaging cytometry software environment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25210731 | OMICS_05634 | SCR_012119 | 2026-08-01 12:04:34 | 0 | |||||||||
|
ISDTool Resource Report Resource Website |
ISDTool (RRID:SCR_012125) | software resource | Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25008418 | OMICS_05696, biotools:isdtool | https://bio.tools/isdtool | SCR_012125 | 2026-08-01 12:04:36 | 0 | ||||||||
|
A5-miseq Resource Report Resource Website 100+ mentions |
A5-miseq (RRID:SCR_012148) | software resource | Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming. | standalone software, illumina, unix/linux, mac os x, bio.tools |
is used by: Nephele is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25338718 | GNU General Public License | OMICS_06339, biotools:a5-miseq | https://bio.tools/a5-miseq | SCR_012148 | 2026-08-01 12:04:34 | 189 | |||||||
|
EC2KEGG Resource Report Resource Website 1+ mentions |
EC2KEGG (RRID:SCR_012127) | software resource | A perl-based package to perform comparative analysis of metabolic pathways between two organisms. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25202338 | OMICS_05782 | SCR_012127 | 2026-08-01 12:04:34 | 8 | |||||||||
|
cnvCapSeq Resource Report Resource Website 1+ mentions |
cnvCapSeq (RRID:SCR_012126) | software resource | Software for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25228465 | GNU Lesser General Public License | OMICS_05722 | SCR_012126 | 2026-08-01 12:04:34 | 2 | ||||||||
|
eALPS Resource Report Resource Website |
eALPS (RRID:SCR_012130) | software resource | Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD). | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24144111 | OMICS_05833 | SCR_012130 | 2026-08-01 12:04:36 | 0 | |||||||||
|
PLEK Resource Report Resource Website 100+ mentions |
PLEK (RRID:SCR_012132) | software resource | An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. | standalone software, roche, pacific biosciences, unix/linux, c, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25239089 | GNU General Public License | biotools:plek, OMICS_05839 | https://bio.tools/plek | SCR_012132 | PLEK: predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme | 2026-08-01 12:04:34 | 122 | ||||||
|
LDx Resource Report Resource Website |
LDx (RRID:SCR_012131) | software resource | A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23152785 | OMICS_05834 | SCR_012131 | 2026-08-01 12:04:34 | 0 |
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