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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SIMULATE Resource Report Resource Website 10+ mentions |
SIMULATE (RRID:SCR_009391) | software application, software resource | Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-dos, vms, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154630, biotools:simulate | https://bio.tools/simulate | SCR_009391 | 2026-02-15 09:20:02 | 11 | |||||||||
|
SASQUANT Resource Report Resource Website 1+ mentions |
SASQUANT (RRID:SCR_013122) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154610, biotools:sasquant | https://bio.tools/sasquant | SCR_013122 | 2026-02-15 09:20:40 | 4 | ||||||||
|
QMSIM Resource Report Resource Website 50+ mentions |
QMSIM (RRID:SCR_013123) | software application, software resource | Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154560, biotools:qmsim | https://bio.tools/qmsim | SCR_013123 | Qtl and Marker SIMulator | 2026-02-15 09:20:38 | 57 | ||||||||
|
LEfSe Resource Report Resource Website 5000+ mentions |
LEfSe (RRID:SCR_014609) | algorithm resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, algorithm, biomarker, genomic feature, web application |
is listed by: Human Microbiome Project is listed by: Debian is listed by: OMICtools |
DOI:10.1186/gb-2011-12-6-r60 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_07818 | https://sources.debian.org/src/lefse/ | SCR_014609 | LDA Effect Size | 2026-02-15 09:20:57 | 7008 | ||||||
|
Fastahack Resource Report Resource Website 1+ mentions |
Fastahack (RRID:SCR_016090) | software application, software resource | Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths. | extract, quickly, subsequence, sequence, FASTA, files, generate, index |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_20516 | https://packages.debian.org/stretch/fastahack https://sources.debian.org/src/fastahack/ |
SCR_016090 | 2026-02-15 09:21:31 | 1 | ||||||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-02-15 09:22:09 | 5 | |||||
|
BioBERT Resource Report Resource Website 10+ mentions |
BioBERT (RRID:SCR_017547) | software application, software resource | Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. | Pretrained, biomedical, language, representation, model, text, mining, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BERT |
National Research Foundation of Korea | DOI:10.1093/bioinformatics/btz682 | Free, Available for download, Freely available | biotools:biobERt | https://github.com/naver/biobert-pretrained https://bio.tools/BioBERT |
SCR_017547 | Bidirectional Encoder Representations from Transformers for Biomedical Text Mining | 2026-02-15 09:22:08 | 45 | |||||
|
MendelIHT.jl Resource Report Resource Website 1+ mentions |
MendelIHT.jl (RRID:SCR_018292) | software application, software resource | Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs. | GWAS, iterative hard thresholding, multiple regression, GLM model, feature selection, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PLINK |
DOI:10.1101/697755 | Free, Available for download, Freely available | biotools:mendeliht.jl | https://bio.tools/mendeliht.jl | SCR_018292 | Mendel Iterative Hard Thresholding.jl, Mendel Iterative Hard Thresholding, MendelIHT | 2026-02-15 09:22:13 | 2 | ||||||
|
BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software application, software resource | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; German Research Foundation ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | Bioconda | 2026-02-15 09:21:35 | 66 | |||||
|
CorrDrugTumorMSI Resource Report Resource Website 1+ mentions |
CorrDrugTumorMSI (RRID:SCR_018962) | software application, software resource | Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data. | Drug, tumor heterogeneity, mass spectrometry imaging, spatial methods, drug distribution correlation, tumor tissue types, MSI, imaging data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:corrdrugtumormsi | https://bio.tools/corrdrugtumormsi | SCR_018962 | 2026-02-15 09:22:25 | 1 | ||||||||
|
GeCo3 Resource Report Resource Website 1+ mentions |
GeCo3 (RRID:SCR_018877) | software application, software resource | Software tool as DNA compressor that uses neural network to do mixing of experts. | DNA compressor, neural network, expert mixing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:geco3 | https://bio.tools/geco3 | SCR_018877 | 2026-02-15 09:22:24 | 2 | ||||||||
|
BayesEpiModels Resource Report Resource Website 1+ mentions |
BayesEpiModels (RRID:SCR_019291) | software application, software resource | Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework. | Stochastic growth model, Stochastic SIR model, Bayesian inference, epidemiological models, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:bayesepimodels | https://bio.tools/bayesepimodels | SCR_019291 | 2026-02-15 09:22:25 | 1 | ||||||||
|
Bio-Chado-Schema Resource Report Resource Website |
Bio-Chado-Schema (RRID:SCR_024059) | software application, software resource | Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module. | Standard object-relational mapping layer, GMOD Chado database schema, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-chado-schema-perl/ | SCR_024059 | libbio-chado-schema-perl, Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema | 2026-02-15 09:23:32 | 0 | ||||||||
|
pyomo Resource Report Resource Website 1+ mentions |
pyomo (RRID:SCR_024188) | software application, software resource | Open source Python-based optimization modeling language with diverse set of optimization capabilities. | Python, optimization modeling language, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pyomo/ | SCR_024188 | 2026-02-15 09:23:22 | 4 | |||||||||
|
AI-FANN Resource Report Resource Website |
AI-FANN (RRID:SCR_024060) | software application, software resource | Software Perl wrapper for the Fast Artificial Neural Network library | Perl wrapper, Fast Artificial Neural Network library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libai-fann-perl/ | SCR_024060 | AI-FANN - Perl wrapper for the Fast Artificial Neural Network library, libai-fann-perl | 2026-02-15 09:22:35 | 0 | ||||||||
|
Bio-Coordinate Resource Report Resource Website |
Bio-Coordinate (RRID:SCR_024063) | software application, software resource | Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. | biological coordinate systems, | is listed by: Debian | https://sources.debian.org/src/libbio-coordinate-perl/ | SCR_024063 | Bio-Coordinate - Modules for working with biological coordinates, libbio-coordinate-perl | 2026-02-15 09:23:32 | 0 | |||||||||
|
Ginkgo CADx Resource Report Resource Website |
Ginkgo CADx (RRID:SCR_024031) | software application, software resource | Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files. | Digital Imaging and Communication In Medicine, DICOM viewer, dicomizer, convert files, png, jpeg, bmp, pdf, tiff, convert to DICOM files, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/ginkgocadx/ https://github.com/gerddie/ginkgocadx |
SCR_024031 | ginkgocadx | 2026-02-15 09:23:31 | 0 | ||||||||
|
HTSJDK Resource Report Resource Website 1+ mentions |
HTSJDK (RRID:SCR_024036) | software application, software resource | Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data. | accessing common file formats, SAM, VCF, manipulating HTS data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htsjdk/ https://github.com/samtools/htsjdk |
SCR_024036 | htsjdk | 2026-02-15 09:22:34 | 2 | ||||||||
|
InsPecT Resource Report Resource Website 1+ mentions |
InsPecT (RRID:SCR_024038) | software application, software resource | Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed. | addresses algorithmic problems, identify modified proteins, post-translational modification identification, | is listed by: Debian | PMID:16013882 | Free, Available for download, Freely available, | OMICS_02397 | https://sources.debian.org/src/inspect/ | SCR_024038 | Inspect, inspect | 2026-02-15 09:23:18 | 1 | ||||||
|
Bibus Resource Report Resource Website |
Bibus (RRID:SCR_023974) | software application, software resource | Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records. | Bibliographic and reference management, bibliographic records, search bibliographic records, edit bibliographic records, sort bibliographic records, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bibus/ | SCR_023974 | bibus | 2026-02-15 09:22:33 | 0 |
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