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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://bio.tools/galactic_circos
Software tool as Galaxy wrapper providing GUI for Circos tool. Circos allows visualizing data in circular format.
Proper citation: Galactic Circos (RRID:SCR_018207) Copy
https://github.com/mridulaprasad/CorrDrugTumorMSI
Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data.
Proper citation: CorrDrugTumorMSI (RRID:SCR_018962) Copy
https://bioinf.shenwei.me/seqkit/
Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.
Proper citation: SeqKit (RRID:SCR_018926) Copy
https://pypi.org/project/jupyter-client/5.2.3/
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.
Proper citation: Jupyter-client (RRID:SCR_018413) Copy
https://CRAN.R-project.org/package=mHG
Software R package to run minimum hypergeometric test.
Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy
https://github.com/HMPNK/CSA2.6
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.
Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy
https://github.com/smithlabcode/riborex
Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.
Proper citation: riborex (RRID:SCR_019104) Copy
https://github.com/jupyter/jupyter_console
Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal.
Proper citation: Jupyter-console (RRID:SCR_018414) Copy
https://github.com/anuprulez/galaxy_tool_recommendation
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.
Proper citation: Tool recommender system in Galaxy (RRID:SCR_018491) Copy
https://github.com/DReichLab/AdmixTools
Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy
https://CRAN.R-project.org/package=openxlsx
Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.
Proper citation: openxlsx (RRID:SCR_019185) Copy
https://github.com/dorianps/LESYMAP
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.
Proper citation: LESYMAP (RRID:SCR_017967) Copy
https://nose.readthedocs.io/en/latest/
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.
Proper citation: Python Nose (RRID:SCR_018418) Copy
https://hoohm.github.io/CITE-seq-Count/
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.
Proper citation: CITE-seq-Count (RRID:SCR_019239) Copy
https://github.com/dorianps/LINDA
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.
Proper citation: LINDA (RRID:SCR_017971) Copy
https://bioconductor.org/packages/release/bioc/html/MetaVolcanoR.html
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.
Proper citation: MetaVolcanoR (RRID:SCR_018549) Copy
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.
Proper citation: PyMC3 (RRID:SCR_018547) Copy
https://www.flidea.tech/flic-support
Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.
Proper citation: FLIC Monitor (RRID:SCR_018387) Copy
https://w3.psychology.su.se/sleipner/
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.
Proper citation: sleipner (RRID:SCR_018143) Copy
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.
Proper citation: Bio2BEL (RRID:SCR_017659) Copy
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