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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Brain Networks Resource Report Resource Website 1+ mentions |
Brain Networks (RRID:SCR_005841) | Brain Networks | data analysis software, software resource, source code, software application, data processing software | Brain Networks: Code to perform network analysis on brain imaging data. | brain, imaging, network analysis, brain imaging, neuroimaging | has parent organization: SourceForge | PMID:21031030 | Open unspecified license - GNU General Public License (GPL) | nlx_149364 | SCR_005841 | brainnetworks | 2026-07-27 09:32:23 | 1 | ||||||
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Maqview Resource Report Resource Website |
Maqview (RRID:SCR_005632) | MaqView | software application, data visualization software, data processing software, software resource | A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License | OMICS_00889, biotools:maqview | https://bio.tools/maqview, https://sources.debian.org/src/maqview/ | SCR_005632 | Mapping and Assembly with Qualities Viewer, M.A.Q Viewer | 2026-07-27 09:32:20 | 0 | |||||
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ESTScan Resource Report Resource Website 100+ mentions |
ESTScan (RRID:SCR_005742) | ESTScan | software application, software resource, data processing software, data analysis software | ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics. | dna, dna sequence, coding region, perl module, c, btlib perl module |
is listed by: Debian is listed by: OMICtools has parent organization: SourceForge |
PMID:10786296 | OMICS_08423, nlx_149202 | https://sources.debian.org/src/estscan/ | SCR_005742 | ESTScan project | 2026-07-27 09:32:21 | 289 | ||||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | service resource, data analysis service, database, analysis service resource, software resource, source code, production service resource, data or information resource | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-07-27 09:32:27 | 0 | |||||
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BLESS Resource Report Resource Website 10+ mentions |
BLESS (RRID:SCR_005963) | BLESS | sequence analysis software, data analysis software, software resource, software application, algorithm resource, data processing software | Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory. | c++, next-generation sequencing, bloom-filter, error correction, ngs, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24451628 | GNU General Public License v3 | OMICS_02246, biotools:bless | https://bio.tools/bless | SCR_005963 | BLoom-filter-based Error correction Solution for high-throughput Sequencing reads, BLESS - Bloom-filter-based Error Correction Tool for NGS reads | 2026-07-27 09:32:25 | 45 | |||||
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Centroid Trajectory Analysis Resource Report Resource Website 10+ mentions |
Centroid Trajectory Analysis (RRID:SCR_006331) | CeTrAn | software application, software resource, data processing software, data analysis software | Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file. | trajectory, buridan, principal components analysis, correlation analysis, buridan's paradigm, locomotion, software, tracking, drosophila |
has parent organization: Free University of Berlin; Berlin; Germany has parent organization: SourceForge |
Swiss National Science Foundation PA00P3_124141; EPSRC EP/F030673/1 |
PMID:22912692 | Open source, Available for Mac and PC, Source code available for download | nlx_152033 | SCR_006331 | CeTrAn: centroid trajectory analysis | 2026-07-27 09:32:31 | 11 | |||||
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BMDExpress Resource Report Resource Website 10+ mentions |
BMDExpress (RRID:SCR_006823) | BMDExpress | software application, software resource, data processing software, data analysis software | Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments. | bioinformatics, microarray, software, toxicogenomics |
is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry has parent organization: SourceForge |
MIT License | nlx_152743 | SCR_006823 | 2026-07-27 09:32:39 | 32 | ||||||||
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Adverse Event Ontology Resource Report Resource Website |
Adverse Event Ontology (RRID:SCR_006807) | AEO | controlled vocabulary, ontology, data or information resource | AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms | has parent organization: SourceForge | nlx_44108 | SCR_006807 | 2026-07-27 09:32:39 | 0 | ||||||||||
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FastSemSim Resource Report Resource Website 1+ mentions |
FastSemSim (RRID:SCR_006919) | FastSemSim | software library, software resource, software toolkit | A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, functional similarity, semantic similarity, graphical user interface, gene ontology, annotation, parse, gene, protein |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Padua; Padua; Italy has parent organization: SourceForge |
Open unspecified license - Free for academic use. GNU GPL license. However, This software is currently unpublished work. You must contact us before using it or its results or any work/app. based on top of it in any published work. | nlx_149309 | SCR_006919 | 2026-07-27 09:32:41 | 6 | ||||||||
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Comparative Data Analysis Ontology Resource Report Resource Website |
Comparative Data Analysis Ontology (RRID:SCR_010297) | CDAO | controlled vocabulary, ontology, data or information resource | A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science | owl, biology, evolution, computer science, comparative analysis, phylogenetic tree, operational taxonomic unit, compared character, molecular |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge |
Public domain | nlx_157371 | http://purl.bioontology.org/ontology/CDAO, http://purl.obolibrary.org/obo/cdao.owl | SCR_010297 | 2026-07-27 09:33:40 | 0 | |||||||
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BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | sequence analysis software, data analysis software, image analysis software, software resource, software application, data processing software, alignment software | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-07-27 09:33:50 | 2291 | |||||
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ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | sequence analysis software, data analysis software, software resource, software application, algorithm resource, data processing software | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-07-27 09:33:58 | 310 | |||||
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TagCleaner Resource Report Resource Website 50+ mentions |
TagCleaner (RRID:SCR_011846) | software application, web application, software resource, standalone software | A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets. | tag sequence, standalone software, web application, microbiome, genomic, metagenomic, datasets |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01094 | SCR_011846 | 2026-07-27 09:33:58 | 63 | |||||||||
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Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | software application, software resource, data processing software, data analysis software | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | Differential alternative splicing events, splicing events calculation, RNA-Seq data, gene isoform ratio, alternative splicing patterns, patterns detection, patterns analysis, replicate RNA-Seq data |
is listed by: OMICtools is listed by: SourceForge has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA |
Free, Available for download, Freely available | OMICS_01336, SCR_020941 | SCR_013049 | RNAseq MATS, RMATS, rMATS, MATS, RNA MATS | 2026-07-27 09:34:19 | 192 | |||||||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, software resource, software application, software development tool, software development environment, portal, data or information resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-07-27 09:34:20 | 24 | ||||
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(at)Note Resource Report Resource Website 1+ mentions |
(at)Note (RRID:SCR_005342) | (at)Note | software application, text-mining software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels. | java, java swt, text, mining |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Minho; Braga; Portugal |
PMID:19393341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01167 | SCR_005342 | (at)Note2 - A workbench for Biomedical Text Mining | 2026-07-27 09:32:15 | 2 | ||||||
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Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | image analysis software, software resource, software application, data processing software, alignment software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-07-27 09:30:51 | 0 | |||||
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Biologic Stylus Resource Report Resource Website |
Biologic Stylus (RRID:SCR_002991) | Biologic Stylus | software application, simulation software, software resource, source code | Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python | bioinformatics, simulation | has parent organization: SourceForge | Free, Available for download, Freely available | nif-0000-30198 | SCR_002991 | biologicstylus | 2026-07-27 09:31:39 | 0 | |||||||
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Hadoop-BAM Resource Report Resource Website 1+ mentions |
Hadoop-BAM (RRID:SCR_005516) | Hadoop-BAM | software library, software resource, software toolkit | A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. | mapreduce/hadoop, java, next generation sequencing data, cloud |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22302568 | MIT License | OMICS_01051 | SCR_005516 | 2026-07-27 09:32:18 | 7 | |||||||
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SPInDel Resource Report Resource Website 1+ mentions |
SPInDel (RRID:SCR_004509) | SPInDel | software resource, data or information resource, data set | A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species. | virus, indel, dna barcoding, alignment, nucleotide sequence, visualization, conserved region, pcr primer, phylogenetic, variant |
is listed by: OMICtools has parent organization: University of Porto; Porto; Portugal has parent organization: SourceForge |
PMID:22978681 PMID:20923781 |
Acknowledgement requested, Free, Public | OMICS_01496 | SCR_004509 | SPecies Identification by Insertions/Deletions, SPInDel - Species identification by insertions/deletions | 2026-07-27 09:32:03 | 2 |
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