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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SeqKit Resource Report Resource Website 100+ mentions |
SeqKit (RRID:SCR_018926) | software toolkit, software resource | Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation. | FASTA file, Q file, file manipulation, fast toolkit | DOI:10.1371/journal.pone.0163962 | Free, Available for download, Freely available | https://github.com/shenwei356/seqkit | SCR_018926 | 2026-08-09 09:07:19 | 210 | |||||||||
|
Jupyter-client Resource Report Resource Website 1+ mentions |
Jupyter-client (RRID:SCR_018413) | software application, software resource | Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels. | Jupyter protocol implementation, Jupyter client library, kernel management API, kernel |
is related to: Jupyter Notebook is related to: Jupyter-core is related to: Jupyter-console |
Free, Freely available | https://github.com/jupyter/jupyter_client/, https://jupyter-client.readthedocs.io/en/stable/ | SCR_018413 | 2026-08-09 09:07:14 | 6 | |||||||||
|
Minimum-Hypergeometric Test Resource Report Resource Website |
Minimum-Hypergeometric Test (RRID:SCR_018776) | mHG | software toolkit, software resource | Software R package to run minimum hypergeometric test. | Minimum hypergeometric test, discovering motif, ranked list, DNA sequence |
is listed by: CRAN is related to: R Project for Statistical Computing |
Gutwirth fellowship ; Agilent PhD Fellowship ; European Union FP6 grant |
PMID:17381235 | Free, Freely available | SCR_018776 | 2026-08-09 09:07:40 | 0 | |||||||
|
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 | 2026-08-09 09:07:10 | 5 | |||||
|
riborex Resource Report Resource Website 1+ mentions |
riborex (RRID:SCR_019104) | software toolkit, software resource | Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency. | Ribo-seq data, differential translation, differential translation identification, mapping genome differences, translation efficiency, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA |
NHGRI R01 HG006015 | PMID:28158331 | Free, Available for download, Freely available | biotools:riborex | https://bio.tools/riborex | SCR_019104 | riborex v2.3.4 | 2026-08-09 09:07:22 | 7 | |||||
|
Jupyter-console Resource Report Resource Website 1+ mentions |
Jupyter-console (RRID:SCR_018414) | software application, software resource | Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal. | Terminal based console, Jupyter kernel, single process IPython terminal, Jupyter Project | is related to: Jupyter-client | Free, Available for download, Freely available | SCR_018414 | Jupyter Terminal Console | 2026-08-09 09:07:42 | 2 | |||||||||
|
Tool recommender system in Galaxy Resource Report Resource Website 1+ mentions |
Tool recommender system in Galaxy (RRID:SCR_018491) | software toolkit, software resource | Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network. | Recommender system, Galaxy, Workflows, Deep learning, Neural networks, Gated recurrent units, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy |
Free, Freely available | biotools:tool_recommender_system_in_galaxy | https://bio.tools/tool_recommender_system_in_galaxy | SCR_018491 | Galaxy tool recommendation, Tool recommender system in Galaxy using deep learning | 2026-08-09 09:07:35 | 2 | |||||||
|
ADMIXTOOLS Resource Report Resource Website 100+ mentions |
ADMIXTOOLS (RRID:SCR_018495) | software toolkit, software resource | Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. | Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard University; Cambridge; United States |
U.S. National Science Foundation HOMINID ; NIGMS GM100233 |
PMID:22960212 | Free, Available for download, Freely available | biotools:admixtools | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html., https://bio.tools/admixtools | SCR_018495 | 2026-08-09 09:07:15 | 222 | ||||||
|
openxlsx Resource Report Resource Website 10+ mentions |
openxlsx (RRID:SCR_019185) | software toolkit, software resource | Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets. | xlsx file, file creation, writing worksheets, styling worksheets, editing worksheets | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/ycphs/openxlsx | SCR_019185 | openxlsx 4.2.3 | 2026-08-09 09:07:23 | 11 | ||||||||
|
LESYMAP Resource Report Resource Website 10+ mentions |
LESYMAP (RRID:SCR_017967) | software toolkit, software resource | Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit. | Conduct, lesion, symptom, mapping, human, MRI, data, cognitive, performance, score, patient, brain, area, deficit | Free, Available for download, Freely available | https://dorianps.github.io/LESYMAP/ | SCR_017967 | Lesion to Symptom Mapping | 2026-08-09 09:07:36 | 14 | |||||||||
|
Python Nose Resource Report Resource Website 1+ mentions |
Python Nose (RRID:SCR_018418) | software application, software resource | Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2. | Testing, extend unittest | Free, Available for download, Freely available | https://github.com/nose-devs/nose/ | SCR_018418 | 2026-08-09 09:07:14 | 1 | ||||||||||
|
CITE-seq-Count Resource Report Resource Website 50+ mentions |
CITE-seq-Count (RRID:SCR_019239) | software toolkit, software resource | Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix. | antibody TAGS count, CITE-seq, cell hashing experiment, antibody derived tags, cell hashing tags, raw sequencing reads, build count matrix, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:https:cite-seq-count | https://cite-seq.com/computational-tools/, https://bio.tools/cite-seq-count | SCR_019239 | CITE-seq-Count v1.4.0, Cellular Indexing of Transcriptomes and Epitopes by Sequencing Count | 2026-08-09 09:07:24 | 60 | |||||||
|
LINDA Resource Report Resource Website 1+ mentions |
LINDA (RRID:SCR_017971) | software toolkit, software resource | Software R package for automated segmentation of chronic stroke lesions. Automated segmentation algorithm capable of learning relationship between existing manual segmentations and single T1-weighted MRI. | Automated, segmentation, chronic, stroke, lesion, algorithm, relationship, existing, manual, single, T1 weighted, MRI | NIDCD R01 DC000191 | PMID:26756101 | Free, Available for download, Freely available | SCR_017971 | Lesion Identification with Neighborhood Data Analysis | 2026-08-09 09:07:27 | 1 | ||||||||
|
MetaVolcanoR Resource Report Resource Website 10+ mentions |
MetaVolcanoR (RRID:SCR_018549) | software toolkit, software resource | Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Differential gene expression, meta analysis, visualization tool, identify gene, gene expression result | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/csbl-usp/MetaVolcanoR | SCR_018549 | 2026-08-09 09:07:15 | 20 | ||||||||||
|
PyMC3 Resource Report Resource Website 50+ mentions |
PyMC3 (RRID:SCR_018547) | software toolkit, software resource | Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code. | Bayesian statistical modeling, probabilistic machine learning, advanced Markov chain Monte Carlo, variational fitting algorithm, model specification, Python code | uses: Python Programming Language | DOI:10.7717/peerj-cs.55 | Free, Freely available | SCR_018547 | 2026-08-09 09:07:43 | 64 | |||||||||
|
FLIC Monitor Resource Report Resource Website 1+ mentions |
FLIC Monitor (RRID:SCR_018387) | software application, software resource | Software tool as user interface for running Fly Liquid Food Interaction Counter experiments. | Monitoring FLIC experiment, monitor fly liquid food experiment, fly liquid food interaction | PMID:24978054 | Free, Available for download, Freely available | SCR_018387 | Fly Liquid Food Interaction Counter Monitor | 2026-08-09 09:07:14 | 2 | |||||||||
|
sleipner Resource Report Resource Website 1+ mentions |
sleipner (RRID:SCR_018143) | software toolkit, software resource | Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm. | Longitudinal data, analysis, cross sectional data, pattern oriented analysis, | has parent organization: Stockholm University; Stockholm; Sweden | Restricted | SCR_018143 | SLEIPNER, Sleipner, SLEIPNER 2.1 | 2026-08-09 09:07:29 | 2 | |||||||||
|
Bio2BEL Resource Report Resource Website 1+ mentions |
Bio2BEL (RRID:SCR_017659) | software toolkit, software resource | Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications. | Biological, expression, language, integration, layer, dataset, biological, database |
uses: PyBEL is listed by: Debian is listed by: bio.tools is related to: Biological Expression Language |
DOI:10.1101/631812 | Free, Available for download, Freely available | biotools:bio2bEL, BioTools:Bio2BEL | https://github.com/bio2bel/bio2bel, https://bio.tools/Bio2BEL, https://bio.tools/Bio2BEL | SCR_017659 | 2026-08-09 09:07:06 | 7 | |||||||
|
org.Rn.eg.db Resource Report Resource Website 1+ mentions |
org.Rn.eg.db (RRID:SCR_018358) | software application, software resource | Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers. | Genome annotation, rat, mapping, Entrez Gene identifier | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018358 | 2026-08-09 09:07:41 | 1 | ||||||||||
|
Condor Resource Report Resource Website 1+ mentions |
Condor (RRID:SCR_017664) | software application, software resource | Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid. | GRID computing software, Distributed Computing Engine, computing, system, maintain, distribute, support | has parent organization: California Institute of Technology; Pasadena; USA | DOI:10.1002/cpe.938 | Free, Freely available | https://research.cs.wisc.edu/htcondor/manual/v7.8/index.html | SCR_017664 | 2026-08-09 09:07:06 | 7 |
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