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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PyBEL Resource Report Resource Website 1+ mentions |
PyBEL (RRID:SCR_017660) | software resource, software toolkit | Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. | Parsing, validating, compiling, converting, network, BEL, biological, expression, language, bio.tools |
is used by: Bio2BEL is listed by: bio.tools is listed by: Debian is related to: Biological Expression Language |
European Union/European Federation of Pharmaceutical Industries and Associations (EFPIA) Innovative Medicines Initiative Joint Undertaking | PMID:29048466 | Free, Available for download, Freely available | biotools:pybel, SCR_024180 | https://github.com/pybel/pybel, https://bio.tools/pybel/, https://pybel.readthedocs.io | https://sources.debian.org/src/python3-pybel/ | SCR_017660 | pybel, Python Biological Expression Language | 2026-08-07 09:28:50 | 1 | ||||
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rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | software resource, software application, data processing software | Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species. | Secondary RNA structures generation, large scale generation, RNA structures, transcriptome folding statistics, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:rna-stability | https://bio.tools/rna-stability | SCR_019259 | 2026-08-07 09:29:11 | 1 | ||||||||
|
RADAR-base Resource Report Resource Website 1+ mentions |
RADAR-base (RRID:SCR_019233) | data or information resource, portal, project portal | Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way. | Data collection, remote data collection, data collection platform, collecting mHealth datasets, mental health, mobile applications, remote sensing technology, telemedicine, bio.tools |
is listed by: bio.tools is listed by: Debian |
GSTT Charity ; Maudsley Charity ; NIHR Biomedical Research Centre at South London ; Maudsley NHS Foundation Trust ; King’s College London ; EU IMI2 ; UK National Institute for Health Research |
Free, Available for download, Freely available | biotools:RADAR-base | https://radar-base.org/index.php/getting-started-with-radar-base/, https://radar-base.org/index.php/getting-started-with-radar-base/demo-using-prmt-app/, https://bio.tools/RADAR-base | SCR_019233 | Remote Assessment of Disease And Relapses, Radar-base | 2026-08-07 09:29:16 | 1 | ||||||
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Atropos Resource Report Resource Website 1+ mentions |
Atropos (RRID:SCR_023962) | software resource, software application, source code | Software tool for specific, sensitive, and speedy trimming of NGS reads. | speedy trimming of NGS reads, NGS reads, Next Generation Sequencing, | is listed by: Debian | PMID:28875074 | Free, Available for download, Freely available | OMICS_20869 | https://sources.debian.org/src/atropos/ | SCR_023962 | atropos | 2026-08-07 09:30:02 | 3 | ||||||
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kempbasu Resource Report Resource Website |
kempbasu (RRID:SCR_024055) | software resource, software toolkit | Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts. | comparing digital gene expression profiles, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kempbasu/ | SCR_024055 | 2026-08-07 09:30:09 | 0 | |||||||||
|
Placnet Resource Report Resource Website |
Placnet (RRID:SCR_024176) | software library, software resource, software toolkit | Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. | plasmid constellation networks, identifies splasmids, visualizes and analyzes plasmids, WGS projects, creating network of contig interactions, comprehensive plasmid analysis within WGS datasets, | is listed by: Debian | PMID:25522143 | Free, Available for download, Freely available, | OMICS_11487 | https://sources.debian.org/src/placnet/ | SCR_024176 | plasmid constellation networks, placnet | 2026-08-07 09:30:11 | 0 | ||||||
|
PRINSEQ Resource Report Resource Website 100+ mentions |
PRINSEQ (RRID:SCR_024178) | software library, software resource, software toolkit | Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format. | data quality control, data preprocessing, genomic and metagenomic datasets, | is listed by: Debian | PMID:21278185 | Free, Available for download, Freely available, | https://sources.debian.org/src/prinseq-lite/ | SCR_024178 | prinseq-lite | 2026-08-07 09:30:12 | 113 | |||||||
|
POA Resource Report Resource Website |
POA (RRID:SCR_024172) | software library, software resource, software toolkit | Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment. | sequence alignment, multiple sequence alignment, handle branching in alignment, handle indels in alignment, | is listed by: Debian | DOI:10.1093/bioinformatics/bth126 | Free, Available for download, Freely available, | OMICS_14254 | https://sources.debian.org/src/poa/ | SCR_024172 | poa, Partial Order Alignment | 2026-08-07 09:30:11 | 0 | ||||||
|
PLIP Resource Report Resource Website 100+ mentions |
PLIP (RRID:SCR_024173) | software library, software resource, software toolkit | Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures. | Protein Ligand Interaction Profiler, | is listed by: Debian | DOI:10.1093/nar/gkv315 | Free, Available for download, Freely available, | OMICS_08028 | https://sources.debian.org/src/plip/, https://github.com/pharmai/plip | SCR_024173 | Protein-Ligand Interaction Profiler, plip | 2026-08-07 09:30:06 | 226 | ||||||
|
CiftiLib Resource Report Resource Website |
CiftiLib (RRID:SCR_023996) | software library, software resource, software toolkit | Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files. | C++, reading and writing files, CIFTI-2, CIFTI-1 | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ciftilib/ | SCR_023996 | ciftilib | 2026-08-07 09:30:02 | 0 | ||||||||
|
Bioparser Resource Report Resource Website 1+ mentions |
Bioparser (RRID:SCR_024065) | software library, software resource, software toolkit | Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files. | C ++, parsing formats, FASTA/Q, MHAP/PAF/SAM, support for zlib compressed files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbioparser-dev/ | SCR_024065 | bioparser, libbioparser-dev | 2026-08-07 09:30:04 | 3 | ||||||||
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pyFAI Resource Report Resource Website 1+ mentions |
pyFAI (RRID:SCR_024186) | software library, software resource, software toolkit | Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. | perform azimuthal integration, two-dimensional regrouping, area detector frames for small and wide angle X-ray scattering experiments, | is listed by: Debian | PMID:25844080 | Free, Available for download, Freely available, | https://sources.debian.org/src/pyfai/ | SCR_024186 | pyfai, pyFai | 2026-08-07 09:30:11 | 9 | |||||||
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BioD Resource Report Resource Website 1+ mentions |
BioD (RRID:SCR_024062) | software library, software resource, software toolkit | Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations. | D library, computational biology and bioinformatics, libbiod, biod, D programming language, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20057 | https://sources.debian.org/src/libbiod/, https://biod.github.io/ | SCR_024062 | BioD | 2026-08-07 09:30:04 | 2 | |||||||
|
CAMP Resource Report Resource Website 1+ mentions |
CAMP (RRID:SCR_023981) | software library, software resource, software toolkit | Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of flexibility to programs, and allows them to fully expose their data structures at runtime. | multi-purpose reflection library | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/camp/ | SCR_023981 | camp | 2026-08-07 09:30:08 | 1 | ||||||||
|
parallel-fastq-dump Resource Report Resource Website 10+ mentions |
parallel-fastq-dump (RRID:SCR_024150) | software library, software resource, software toolkit | Software wrapper to speed up downloading process by dividing the work into multiple threads. | wrapper, speed up downloading process, dividing the work into multiple threads, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/parallel-fastq-dump/ | SCR_024150 | 2026-08-07 09:30:11 | 16 | |||||||||
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GfaPy Resource Report Resource Website |
GfaPy (RRID:SCR_024030) | software library, software resource, software toolkit | Software library for handling sequence graphs in Python. | sequence graphs, Python | is listed by: Debian | PMID:28645150 | Free, Available for download, Freely available, | OMICS_19577 | https://sources.debian.org/src/gfapy/ | SCR_024030 | gfapy, Gfapy | 2026-08-07 09:30:09 | 0 | ||||||
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BioImageXD Resource Report Resource Website 10+ mentions |
BioImageXD (RRID:SCR_023979) | software resource, software toolkit | Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. | post-processing tool, bioimaging, visualization, multi-channel temporal image stacks, 3D rendering of multiple channels at once, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bioimagexd/ | SCR_023979 | bioimagexd | 2026-08-07 09:30:09 | 26 | ||||||||
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BAli-Phy Resource Report Resource Website |
BAli-Phy (RRID:SCR_023976) | software resource, software application, source code | Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously. | estimate multiple sequence alignments, estimate evolutionary trees, DNA sequences, amino acid sequences, codon sequences, | is listed by: Debian | PMID:16679334 PMID:33677478 |
Free, Available for download, Freely available | OMICS_03734 | https://sources.debian.org/src/bali-phy/ | SCR_023976 | bali-phy, BAli-Phy version 3 | 2026-08-07 09:30:08 | 0 | ||||||
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OptimiR Resource Report Resource Website |
OptimiR (RRID:SCR_024149) | software library, software resource, software toolkit | Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis. | miRSeq data alignment workflow, integrate genetic information, assess impact of variants, miRNA expression, integrating genome wide genotype data, miRNA sequence alignment analysis, | is listed by: Debian | PMID:30819774 | Free, Available for download, Freely available, | OMICS_33123 | https://sources.debian.org/src/optimir/ | SCR_024149 | optimir | 2026-08-07 09:30:06 | 0 | ||||||
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Intake Resource Report Resource Website |
Intake (RRID:SCR_024042) | software resource, software toolkit | Software package for finding, investigating, loading and disseminating data. | finding data, investigating data, loading data, disseminating data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/intake/, https://intake.readthedocs.io/en/latest/ | SCR_024042 | Intake: A general interface for loading data, intake | 2026-08-07 09:30:09 | 0 |
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